variant_id sample_id genome_build lower_chr lower_bkpt lower_strand higher_chr higher_bkpt higher_strand microhomology_length microhomology_motif NTS_length NTS_motif Gene_build lower_bkpt_context higher_bkpt_context lower_gene higher_gene lower_gene_id higher_gene_id lower_trans_id higher_trans_id lower_gene_strand higher_gene_strand lower_entrez_id higher_entrez_id variant_type confirmation_status alignment_software validation_platform brass_read_count old_read_count paired_flag 34751672 PD3851a NCBI-37 12 66552286 + 20 56900158 + 0 59 TGCGTGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTAAACCT Ensembl58 intron1 intron2 TMBIM4 RAB22A ENSG00000155957 ENSG00000124209 ENST00000358230 ENST00000244040 -1 1 51643 57403 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 34823970 PD3851a NCBI-37 15 52100678 - 20 52465052 + 0 3 TGA Ensembl58 3UTR intergenic TMOD2 ENSG00000128872 ENST00000249700 1 29767 interchromosomal somatic BWA-0.5.8 BRASS-0 13 32 IL24_4172:1:51:11895:8474 PD3851a NCBI-37 16 13782796 - 16 19394219 - 2 CA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 IL24_4172:6:1:9695:20787 PD3851a NCBI-37 16 17480155 + 16 19411315 + 0 0 Ensembl58 intron1 intergenic XYLT1 ENSG00000103489 ENST00000261381 -1 64131 deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 IL24_4172:6:64:3081:14894 PD3851a NCBI-37 16 25851272 - 16 27811542 + 0 0 Ensembl58 intron1 intron6 HS3ST4 GSG1L ENSG00000182601 ENSG00000169181 ENST00000331351 ENST00000447459 1 -1 9951 146395 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 6 8 34834213/IL24_4172:2:87:1958:7589 PD3851a NCBI-37 16 4489860 + 16 27812218 - 0 1 C Ensembl58 intron3 intron6 DNAJA3 GSG1L ENSG00000103423 ENSG00000169181 ENST00000355296 ENST00000447459 1 -1 9093 146395 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 24 3 1 34837246 PD3851a NCBI-37 16 19393677 - 20 59352203 + 1 T 0 Ensembl58 intergenic intron7 ENSG00000237240 ENSG00000237240 ENST00000456299 1 interchromosomal somatic BWA-0.5.8 BRASS-0 45 32 34840979/IL24_4172:7:1:17450:6244 PD3851a NCBI-37 16 31046819 + 20 47799295 + 2 AT 0 Ensembl58 intron5 intron1 STX4 STAU1 ENSG00000103496 ENSG00000124214 ENST00000313843 ENST00000371856 1 -1 6810 6780 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 23 7 32 IL24_4172:3:22:7035:19097 PD3851a NCBI-37 20 54011659 + 20 57351882 - 0 0 Ensembl58 intergenic intron3 ENSG00000237121 ENSG00000237121 ENST00000416241 -1 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 2 1 IL24_4172:2:55:6556:10085 PD3851a NCBI-37 20 54641857 - 20 56661349 - 3 TCA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 EAS192_92:4:82:378:804 PD3890a NCBI-37 1 110571696 - 1 110599546 - 2 CT 0 Ensembl58 intergenic intron12 FAM40A ENSG00000143093 ENST00000473429 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:6:68:1397:442 PD3890a NCBI-37 1 154767539 - 1 154776291 - 1 T 0 Ensembl58 intron2 intron2 KCNN3 KCNN3 ENSG00000143603 ENSG00000143603 ENST00000271915 ENST00000271915 -1 -1 3782 3782 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 21117181 PD3890a NCBI-37 1 165407138 - 1 209894824 - 4 TTTT 0 Ensembl58 intron1 intron5 RXRG HSD11B1 ENSG00000143171 ENSG00000117594 ENST00000359842 ENST00000261465 -1 1 6258 3290 tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 EAS192_92:6:64:306:834 PD3890a NCBI-37 1 168615340 - 1 168619456 - 1 A 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:2:48:601:1537 PD3890a NCBI-37 1 178112724 - 1 178177831 - 0 0 Ensembl58 intron1 intron1 RASAL2 RASAL2 ENSG00000075391 ENSG00000075391 ENST00000263528 ENST00000263528 1 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:7:68:919:990 PD3890a NCBI-37 1 183435178 + 1 183436380 + 0 8 GGCAACAT Ensembl58 intron3 intron3 ENSG00000232860 ENSG00000232860 ENSG00000232860 ENSG00000232860 ENST00000421703 ENST00000421703 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 EAS56_153:7:49:662:1452 PD3890a NCBI-37 1 185985807 - 1 186007268 - 4 ATAA 0 Ensembl58 intron32 intron37 HMCN1 HMCN1 ENSG00000143341 ENSG00000143341 ENST00000271588 ENST00000271588 1 1 83872 83872 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 EAS192_92:7:82:420:475 PD3890a NCBI-37 1 204403142 - 1 204407802 - 2 TG 0 Ensembl58 intron25 intron24 PIK3C2B PIK3C2B ENSG00000133056 ENSG00000133056 ENST00000367187 ENST00000367187 -1 -1 5287 5287 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 EAS192_92:8:9:275:696 PD3890a NCBI-37 1 211917130 - 1 211934321 - 0 2 AG Ensembl58 3UTR intron6 LPGAT1 LPGAT1 ENSG00000123684 ENSG00000123684 ENST00000366997 ENST00000366997 -1 -1 9926 9926 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS192_92:8:22:1850:511 PD3890a NCBI-37 1 229940689 - 1 229951529 - 3 CAT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 EAS192_92:2:4:629:1930 PD3890a NCBI-37 1 235139943 - 1 235296745 - 2 CC 0 Ensembl58 intergenic intron10 RBM34 ENSG00000188739 ENST00000366606 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS192_92:4:24:1233:6 PD3890a NCBI-37 1 247000527 - 1 247005472 - 2 TG 0 Ensembl58 intron1 intron34 ENSG00000249794 AHCTF1 ENSG00000249794 ENSG00000153207 ENST00000504864 ENST00000391829 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 EAS56_153:6:89:1386:1719 PD3890a NCBI-37 1 26792544 - 1 26806740 - 0 0 Ensembl58 intron8 intergenic DHDDS ENSG00000117682 ENST00000360009 1 79947 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:7:70:695:1442 PD3890a NCBI-37 1 44143030 - 1 44162623 - 2 TT 0 Ensembl58 intron11 intron18 KDM4A KDM4A ENSG00000066135 ENSG00000066135 ENST00000372396 ENST00000372396 1 1 9682 9682 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS192_92:6:68:1213:1175 PD3890a NCBI-37 1 66690752 + 1 66831880 + 0 0 Ensembl58 intron2 intron12 PDE4B PDE4B ENSG00000184588 ENSG00000184588 ENST00000371049 ENST00000371049 1 1 5142 5142 deletion somatic MAQ-0.7.1 capillary_sequencing 10 2 EAS56_153:2:66:1508:359 PD3890a NCBI-37 1 66838567 - 1 66874083 - 3 CAA 0 Ensembl58 3UTR intergenic PDE4B ENSG00000184588 ENST00000371045 1 5142 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 21097566 PD3890a NCBI-37 1 93997852 + 1 114433281 + 2 CC 0 Ensembl58 intron7 intron3 FNBP1L ENSG00000226167 ENSG00000137942 ENSG00000226167 ENST00000370253 ENST00000419536 1 1 deletion somatic BWA-0.5.8 BRASS-0 8 2 21089930/EAS56_153:1:91:822:32 PD3890a NCBI-37 1 36085155 - 10 15216835 - 2 AG 0 Ensembl58 intron3 intron1 PSMB2 ENSG00000248743 ENSG00000126067 ENSG00000248743 ENST00000373237 ENST00000512032 -1 1 5690 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 4 32 EAS56_153:3:41:1037:414 PD3890a NCBI-37 10 114884545 - 10 114898398 - 0 5 TAATA Ensembl58 intron4 intron4 TCF7L2 TCF7L2 ENSG00000148737 ENSG00000148737 ENST00000369397 ENST00000369397 1 1 6934 6934 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 EAS56_153:8:16:25:380 PD3890a NCBI-37 10 1661020 - 10 1668152 - 2 TT 0 Ensembl58 intron1 intron1 ADARB2 ADARB2 ENSG00000185736 ENSG00000185736 ENST00000381312 ENST00000381312 -1 -1 105 105 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 EAS56_153:3:3:343:63 PD3890a NCBI-37 10 34192385 - 10 34196930 - 1 T 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:7:64:1621:638 PD3890a NCBI-37 10 89674132 - 10 89692150 - 3 GCA 0 Ensembl58 intron2 intron4 PTEN PTEN ENSG00000171862 ENSG00000171862 ENST00000371953 ENST00000371953 1 1 5728 5728 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS192_92:1:40:1553:995 PD3890a NCBI-37 10 94062722 + 10 94063930 - 5 CATTT 0 Ensembl58 intron1 intron1 Mar-05 Mar-05 ENSG00000198060 ENSG00000198060 ENST00000358935 ENST00000358935 1 1 54708 54708 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 21303687/EAS56_153:8:12:892:907 PD3890a NCBI-37 10 98705365 - 10 106157580 + 1 C 0 Ensembl58 intron5 intron11 LCOR CCDC147 ENSG00000196233 ENSG00000120051 ENST00000371103 ENST00000369704 1 1 84458 159686 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 6 8 8 21296844 PD3890a NCBI-37 10 23694782 - 16 74820549 - 0 0 Ensembl58 intron1 intergenic ENSG00000224148 ENSG00000224148 ENST00000451785 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 11 32 EAS56_153:6:26:965:621 PD3890a NCBI-37 10 96632973 + 17 80790576 + 0 12 GGTGTCAGGACA Ensembl58 intergenic intron1 ZNF750 ENSG00000141579 ENST00000269394 -1 79755 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 9 32 EAS192_92:3:59:1682:1892 PD3890a NCBI-37 11 102317724 - 11 102387775 - 1 C 0 Ensembl58 intron2 intergenic TMEM123 ENSG00000152558 ENST00000398136 -1 114908 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 EAS56_153:8:21:355:563 PD3890a NCBI-37 11 115387538 - 11 115389679 - 2 TA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:7:51:535:1655 PD3890a NCBI-37 11 12741296 - 11 12841126 - 3 CAG 0 Ensembl58 intron2 intron3 TEAD1 TEAD1 ENSG00000187079 ENSG00000187079 ENST00000361905 ENST00000361905 1 1 7003 7003 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:2:98:1157:1922 PD3890a NCBI-37 11 16734451 + 11 16737137 + 3 AAA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 EAS56_153:6:48:1227:169 PD3890a NCBI-37 11 33894465 + 11 33898104 + 1 G 0 Ensembl58 intron2 intron2 LMO2 LMO2 ENSG00000135363 ENSG00000135363 ENST00000257818 ENST00000257818 -1 -1 4005 4005 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 EAS56_153:6:14:942:1732 PD3890a NCBI-37 11 6763968 + 11 6771429 + 0 5 ACTGA Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 EAS192_92:3:1:1264:1974 PD3890a NCBI-37 11 78334627 - 11 127318438 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:1:39:450:514 PD3890a NCBI-37 11 81956286 - 11 81968633 - 2 CT 0 Ensembl58 intron3 intron3 ENSG00000245832 ENSG00000245832 ENSG00000245832 ENSG00000245832 ENST00000500502 ENST00000500502 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 21312706 PD3890a NCBI-37 11 95404785 + 11 101766421 + 1 A 0 Ensembl58 intergenic intron7 ANGPTL5 ENSG00000187151 ENST00000334289 -1 253935 deletion somatic BWA-0.5.8 BRASS-0 7 2 EAS192_92:1:90:1702:1103 PD3890a NCBI-37 12 12876862 + 12 12879319 + 0 0 Ensembl58 intergenic intron1 APOLD1 ENSG00000178878 ENST00000326765 1 81575 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 21316257 PD3890a NCBI-37 12 15004911 + 12 20297531 + 1 A 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 15 2 EAS56_153:8:32:1437:1011 PD3890a NCBI-37 12 20725730 - 12 20732634 - 0 15 ATCCCAACTACATGA Ensembl58 intron2 intron2 PDE3A PDE3A ENSG00000172572 ENSG00000172572 ENST00000359062 ENST00000359062 1 1 5139 5139 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 11 4 EAS56_153:1:63:1567:1907 PD3890a NCBI-37 12 22236544 - 12 22243246 - 2 CA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 EAS56_153:4:10:1410:1092 PD3890a NCBI-37 12 63084050 - 12 63096551 - 0 4 CACT Ensembl58 intron7 intron6 PPM1H PPM1H ENSG00000111110 ENSG00000111110 ENST00000228705 ENST00000228705 -1 -1 57460 57460 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 EAS56_153:5:95:1567:1265 PD3890a NCBI-37 12 6857006 - 12 6865150 - 1 G 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS192_92:4:54:1497:1621 PD3890a NCBI-37 13 73519490 + 13 73520207 + 1 A 0 Ensembl58 intron14 intron14 PIBF1 PIBF1 ENSG00000083535 ENSG00000083535 ENST00000326291 ENST00000326291 1 1 10464 10464 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 21325022/EAS56_153:8:12:742:665 PD3890a NCBI-37 13 72456916 - 21 37523754 - 4 AGCA 0 Ensembl58 intergenic intron1 ENSG00000236830 ENSG00000236830 ENST00000427491 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 13 4 32 EAS192_92:3:99:381:560 PD3890a NCBI-37 14 21177547 - 14 21182237 - 1 C 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 21329095 PD3890a NCBI-37 14 25732719 - 14 33952057 - 6 AAAGAA 0 Ensembl58 intergenic intron3 NPAS3 ENSG00000151322 ENST00000346562 1 64067 tandem_duplication somatic BWA-0.5.8 BRASS-0 9 4 EAS56_153:7:32:1361:1357 PD3890a NCBI-37 14 33236778 - 14 33488181 - 2 TA 0 Ensembl58 intron11 intron1 AKAP6 NPAS3 ENSG00000151320 ENSG00000151322 ENST00000280979 ENST00000346562 1 1 9472 64067 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 EAS56_153:6:99:236:171 PD3890a NCBI-37 14 65671953 - 14 65677504 - 1 G 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS192_92:5:63:745:1040 PD3890a NCBI-37 15 48236884 - 15 48240395 - 1 A 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:2:99:1299:1267 PD3890a NCBI-37 16 527378 - 16 536682 - 4 GTCA 0 Ensembl58 intron3 intron4 RAB11FIP3 RAB11FIP3 ENSG00000090565 ENSG00000090565 ENST00000262305 ENST00000262305 1 1 9727 9727 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 EAS192_92:1:93:904:111 PD3890a NCBI-37 16 53315396 - 16 53320527 - 4 AGAA 0 Ensembl58 intron24 intron26 CHD9 CHD9 ENSG00000177200 ENSG00000177200 ENST00000398510 ENST00000398510 1 1 80205 80205 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:1:60:1485:361 PD3890a NCBI-37 16 69483218 - 16 69491104 - 0 22 GAAATATTTTGTAATTTCCATT Ensembl58 intron3 intron3 CYB5B CYB5B ENSG00000103018 ENSG00000103018 ENST00000307892 ENST00000307892 1 1 80777 80777 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 EAS192_92:2:87:1655:1726 PD3890a NCBI-37 16 71576436 - 16 71583717 - 3 CCA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS192_92:2:7:861:531 PD3890a NCBI-37 17 28266671 - 17 28277172 - 0 7 TTCCTTA Ensembl58 intron1 intron3 EFCAB5 EFCAB5 ENSG00000176927 ENSG00000176927 ENST00000448319 ENST00000448319 1 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS192_92:2:27:850:1586 PD3890a NCBI-37 17 33957602 - 17 33966030 - 0 0 Ensembl58 intron9 intron10 AP2B1 AP2B1 ENSG00000006125 ENSG00000006125 ENST00000312678 ENST00000312678 1 1 163 163 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:8:35:1566:1634 PD3890a NCBI-37 17 61482498 + 17 61485798 - 0 2 TG Ensembl58 exon18 intron19 TANC2 TANC2 ENSG00000170921 ENSG00000170921 ENST00000424789 ENST00000424789 1 1 26115 26115 deletion somatic MAQ-0.7.1 capillary_sequencing 8 2 EAS56_153:6:9:371:243 PD3890a NCBI-37 17 66848023 - 17 66851481 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 12 4 EAS56_153:8:56:1488:797 PD3890a NCBI-37 18 18864895 + 18 18869597 - 4 AATA 0 Ensembl58 intron1 intron1 GREB1L GREB1L ENSG00000141449 ENSG00000141449 ENST00000424526 ENST00000424526 1 1 80000 80000 deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 EAS56_153:2:26:1335:967 PD3890a NCBI-37 18 4218899 - 18 4224074 - 3 TGT 0 Ensembl58 intron1 intron1 ENSG00000250093 ENSG00000250093 ENSG00000250093 ENSG00000250093 ENST00000515196 ENST00000515196 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:5:13:1084:309 PD3890a NCBI-37 19 58748086 - 19 58793851 - 2 AT 0 Ensembl58 intron3 intron1 ZNF544 ZNF8 ENSG00000198131 ENSG00000083842 ENST00000269829 ENST00000196548 1 1 27300 7554 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 EAS192_92:1:17:933:1478 PD3890a NCBI-37 2 100213793 + 2 100218157 - 2 CA 0 Ensembl58 intron13 intron12 AFF3 AFF3 ENSG00000144218 ENSG00000144218 ENST00000356421 ENST00000356421 -1 -1 3899 3899 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 11 1 EAS192_92:2:2:544:1791 PD3890a NCBI-37 2 100216170 - 2 100218026 + 0 0 Ensembl58 intron13 exon13 AFF3 AFF3 ENSG00000144218 ENSG00000144218 ENST00000356421 ENST00000356421 -1 -1 3899 3899 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 EAS192_92:3:60:1003:1119 PD3890a NCBI-37 2 161882926 - 2 162029627 - 0 3 TTA Ensembl58 intergenic intron1 TANK ENSG00000136560 ENST00000454334 1 10010 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 21158314 PD3890a NCBI-37 2 197086416 + 2 228922868 + 0 11 CCAGTTGACAT Ensembl58 intron24 intron3 HECW2 SPHKAP ENSG00000138411 ENSG00000153820 ENST00000260983 ENST00000344657 -1 -1 57520 80309 deletion somatic BWA-0.5.8 BRASS-0 4 2 21158658/EAS56_153:8:26:1640:906 PD3890a NCBI-37 2 200988224 - 2 206344009 - 0 0 Ensembl58 intergenic intron19 PARD3B ENSG00000116117 ENST00000349953 1 117583 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 11 4 EAS56_153:1:50:262:557 PD3890a NCBI-37 2 202139773 - 2 202152293 - 0 0 Ensembl58 intron6 3UTR CASP8 CASP8 ENSG00000064012 ENSG00000064012 ENST00000358485 ENST00000358485 1 1 841 841 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:7:76:561:1844 PD3890a NCBI-37 2 219604558 - 2 219609605 - 1 C 0 Ensembl58 intron1 intron3 TTLL4 TTLL4 ENSG00000135912 ENSG00000135912 ENST00000258398 ENST00000258398 1 1 9654 9654 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 13 4 EAS192_92:2:9:1143:336 PD3890a NCBI-37 2 46159194 - 2 46167453 - 5 CATCT 0 Ensembl58 intron2 intron2 PRKCE PRKCE ENSG00000171132 ENSG00000171132 ENST00000306156 ENST00000306156 1 1 5581 5581 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 13 4 EAS192_92:4:97:1805:1217 PD3890a NCBI-37 2 61516810 - 2 61537686 - 4 TGCT 0 Ensembl58 intron33 intron27 USP34 USP34 ENSG00000115464 ENSG00000115464 ENST00000398571 ENST00000398571 -1 -1 9736 9736 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:1:10:820:1927 PD3890a NCBI-37 20 19843318 - 20 19981962 - 2 AG 0 Ensembl58 intergenic RIN2 ENSG00000132669 ENST00000484638 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 EAS192_92:3:49:1348:421 PD3890a NCBI-37 20 46871560 - 20 46876094 - 3 CTG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS192_92:1:20:799:813 PD3890a NCBI-37 3 119237624 + 3 119238984 + 0 0 Ensembl58 intron6 intron6 C3orf1 C3orf1 ENSG00000113845 ENSG00000113845 ENST00000494664 ENST00000494664 1 1 51300 51300 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 EAS56_153:7:68:1633:1509 PD3890a NCBI-37 3 135526835 - 3 135720592 - 0 1 A Ensembl58 intergenic exon2 PPP2R3A ENSG00000073711 ENST00000264977 1 5523 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:6:16:1344:1738 PD3890a NCBI-37 3 139336883 - 3 139341805 - 0 0 Ensembl58 intron3 intron3 NMNAT3 NMNAT3 ENSG00000163864 ENSG00000163864 ENST00000406164 ENST00000406164 -1 -1 349565 349565 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 EAS56_153:1:94:809:1931 PD3890a NCBI-37 3 148107127 + 3 148231900 + 2 GT 0 Ensembl58 intron2 intergenic ENSG00000242440 ENSG00000242440 ENST00000481334 1 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 EAS56_153:7:60:241:1214 PD3890a NCBI-37 3 176292379 + 3 176294557 + 3 GTT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 21166536/EAS192_92:3:100:776:1706 PD3890a NCBI-37 3 31045406 + 3 37603147 + 1 C 0 Ensembl58 intergenic intron15 ITGA9 ENSG00000144668 ENST00000264741 1 3680 deletion somatic MAQ-0.7.1 capillary_sequencing 3 5 2 21167155/EAS56_153:5:86:16:1851 PD3890a NCBI-37 3 37998458 + 3 55228608 + 2 GG 0 Ensembl58 intron2 intergenic CTDSPL ENSG00000144677 ENST00000273179 1 10217 deletion somatic MAQ-0.7.1 capillary_sequencing 6 3 2 EAS56_153:2:45:696:1808 PD3890a NCBI-37 3 85103836 + 3 85107457 + 0 1 T Ensembl58 intron1 intron1 ENSG00000237789 CADM2 ENSG00000237789 ENSG00000175161 ENST00000446809 ENST00000407528 -1 1 253559 deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 EAS56_153:1:96:1789:1114 PD3890a NCBI-37 3 135527172 + 4 167322932 - 0 0 Ensembl58 intergenic intron3 ENSG00000249675 ENSG00000249675 ENST00000514134 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 32 21184621 PD3890a NCBI-37 3 195882957 + 4 126949443 + 3 AGT 0 Ensembl58 intron2 intergenic ENSG00000224652 ENSG00000224652 ENST00000457079 1 interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 EAS56_153:8:41:1332:1667 PD3890a NCBI-37 3 172536375 - X 3962570 + 2 AA 0 Ensembl58 intron22 intergenic ECT2 ENSG00000114346 ENST00000441497 1 1894 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 9 32 EAS56_153:7:31:1733:500 PD3890a NCBI-37 4 188053140 - 11 6853761 - 3 GAG 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 32 EAS192_92:8:92:886:1785 PD3890a NCBI-37 4 120948572 + 18 77184607 - 1 G 0 Ensembl58 intergenic intron2 NFATC1 ENSG00000131196 ENST00000329101 1 4772 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 EAS192_92:6:80:1305:1804 PD3890a NCBI-37 4 120949138 - 18 77184056 + 5 ATTTT 0 Ensembl58 intergenic intron2 NFATC1 ENSG00000131196 ENST00000329101 1 4772 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 EAS192_92:4:24:978:654 PD3890a NCBI-37 4 148073113 - 4 148091141 - 2 GC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:8:11:983:1430 PD3890a NCBI-37 4 153773212 - 4 153778609 - 4 TTAA 0 Ensembl58 intron2 intron2 ARFIP1 ARFIP1 ENSG00000164144 ENSG00000164144 ENST00000353617 ENST00000353617 1 1 27236 27236 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 21192455 PD3890a NCBI-37 4 54558716 - 4 110161204 - 1 A 0 Ensembl58 intron2 intron3 LNX1 COL25A1 ENSG00000072201 ENSG00000188517 ENST00000513421 ENST00000399126 -1 -1 84570 tandem_duplication somatic BWA-0.5.8 BRASS-0 13 4 21203491/EAS56_153:1:60:564:279 PD3890a NCBI-37 4 138678841 + 5 32559531 - 0 1 T Ensembl58 intergenic intron2 SUB1 ENSG00000113387 ENST00000513013 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 5 32 21189226 PD3890a NCBI-37 4 39840127 - 6 2644856 - 0 1 T Ensembl58 intron31 intergenic PDS5A ENSG00000121892 ENST00000412404 -1 23244 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 21226916 PD3890a NCBI-37 5 171137273 - 16 889078 + 3 CTT 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 EAS192_92:2:94:1860:373 PD3890a NCBI-37 5 2433799 - 20 44792767 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 21212295/EAS56_153:4:9:545:106 PD3890a NCBI-37 5 14076302 + 5 26468220 + 9 AAGAGAGCA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 2 EAS56_153:3:41:458:360 PD3890a NCBI-37 5 147440257 - 5 147451118 - 1 A 0 Ensembl58 intergenic intron3 SPINK5 ENSG00000133710 ENST00000256084 1 11005 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 21211398 PD3890a NCBI-37 5 3967851 + 5 33995375 + 3 AGG 0 Ensembl58 intergenic intron3 AMACR ENSG00000242110 ENST00000506639 -1 deletion somatic BWA-0.5.8 BRASS-0 14 2 EAS56_153:8:25:310:1808 PD3890a NCBI-37 5 91298144 - 5 91300892 - 4 TCTT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 EAS192_92:7:4:1114:1183 PD3890a NCBI-37 5 96080017 - 5 96106652 - 0 0 Ensembl58 intron15 intron29 CAST CAST ENSG00000153113 ENSG00000153113 ENST00000359176 ENST00000359176 1 1 831 831 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 EAS192_92:5:84:568:1191 PD3890a NCBI-37 6 113331215 - 6 113336134 - 0 2 GG Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 21240132/EAS56_153:1:29:1203:1512 PD3890a NCBI-37 6 131063842 - 6 138829405 - 1 C 0 Ensembl58 intergenic intron1 NHSL1 ENSG00000135540 ENST00000491526 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 7 4 EAS56_153:8:24:1651:293 PD3890a NCBI-37 6 133628933 - 6 133634762 - 2 AA 0 Ensembl58 intron2 intron2 EYA4 EYA4 ENSG00000112319 ENSG00000112319 ENST00000355167 ENST00000355167 1 1 2070 2070 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:8:20:430:116 PD3890a NCBI-37 6 158536165 - 6 158544692 - 1 G 0 Ensembl58 intron14 intron10 SERAC1 SERAC1 ENSG00000122335 ENSG00000122335 ENST00000367104 ENST00000367104 -1 -1 84947 84947 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:8:18:966:219 PD3890a NCBI-37 6 47829394 - 6 48185229 + 2 TA 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 7 8 EAS56_153:2:3:1628:13 PD3890a NCBI-37 6 47833314 + 6 48193166 - 1 T 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 EAS56_153:1:59:95:1314 PD3890a NCBI-37 6 50661433 - 6 50663461 - 1 T 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:2:30:1461:1067 PD3890a NCBI-37 6 73561358 - 6 73571765 - 3 CAC 0 Ensembl58 intron1 intron1 KCNQ5 KCNQ5 ENSG00000185760 ENSG00000185760 ENST00000370398 ENST00000370398 1 1 56479 56479 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS192_92:5:8:93:1901 PD3890a NCBI-37 7 44615959 - 10 79124138 + 2 GA 0 Ensembl58 intergenic intron2 KCNMA1 ENSG00000156113 ENST00000286627 -1 3778 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 EAS56_153:7:73:550:75 PD3890a NCBI-37 7 152032446 + 11 6853083 + 1 T 0 Ensembl58 intron2 intergenic BAGE3 ENSG00000055609 ENST00000262189 -1 58508 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 EAS56_153:7:88:1764:1140 PD3890a NCBI-37 7 152021363 - 7 152032445 + 0 228 ACAGGTTGCAGATATGCATCCCAGTTTTGTAAACTGGAGGCTTGACCAATAGCTGATACATACCTAGCAAACAACACTTCTGTTCAGCGTTTAGTAGGGAAAACTCTTCTTACTGTTACCAGCAAAGCGACAGTTACGGGTTCAATTTGTCATAAAGCTTTGTCTACCCCCAGGACTGGTTGTTTCATCAGGGAATAGTTAGGTTTCAGCATCCTTTCGTTGTTGTGA Ensembl58 intron3 intron2 BAGE3 BAGE3 ENSG00000055609 ENSG00000055609 ENST00000262189 ENST00000262189 -1 -1 58508 58508 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS192_92:1:33:885:96 PD3890a NCBI-37 7 17807891 - 7 17830782 - 1 T 0 Ensembl58 intergenic 3UTR SNX13 ENSG00000071189 ENST00000242044 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 EAS56_153:7:67:402:969 PD3890a NCBI-37 7 31741280 - 7 31745319 - 2 TT 0 Ensembl58 intron3 intron3 C7orf16 C7orf16 ENSG00000106341 ENSG00000106341 ENST00000409146 ENST00000409146 1 1 10842 10842 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 EAS56_153:7:95:1262:1435 PD3890a NCBI-37 7 36321794 - 7 36326641 - 2 CC 0 Ensembl58 intron4 intron5 EEPD1 EEPD1 ENSG00000122547 ENSG00000122547 ENST00000242108 ENST00000242108 1 1 80820 80820 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 EAS56_153:8:70:797:1286 PD3890a NCBI-37 7 52034868 - 7 52039613 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 EAS192_92:3:54:700:791 PD3890a NCBI-37 8 18775028 - 14 21846500 + 0 4 CCTC Ensembl58 intron2 intron1 PSD3 SUPT16H ENSG00000156011 ENSG00000092201 ENST00000327040 ENST00000216297 -1 -1 23362 11198 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 21276163 PD3890a NCBI-37 8 145967252 + 21 45014584 + 2 AA 0 Ensembl58 intron4 intron7 ZNF251 HSF2BP ENSG00000198169 ENSG00000160207 ENST00000292562 ENST00000291560 -1 -1 90987 11077 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 EAS56_153:6:41:1784:2011 PD3890a NCBI-37 8 128546599 - 8 128639262 + 4 CTAT 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 10 8 EAS56_153:7:86:1328:1863 PD3890a NCBI-37 8 128638315 - 8 128727821 - 1 C 0 Ensembl58 intergenic intron1 ENSG00000249375 ENSG00000249375 ENST00000502463 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 13 4 EAS192_92:6:79:292:1283 PD3890a NCBI-37 8 141400360 - 8 141678652 - 1 C 0 Ensembl58 intron7 intron29 TRAPPC9 PTK2 ENSG00000167632 ENSG00000169398 ENST00000389328 ENST00000340930 -1 -1 83696 5747 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 EAS56_153:8:40:662:1154 PD3890a NCBI-37 8 141903476 - 8 141908774 - 0 6 ATGTTC Ensembl58 intron2 intron2 PTK2 PTK2 ENSG00000169398 ENSG00000169398 ENST00000340930 ENST00000340930 -1 -1 5747 5747 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 EAS192_92:4:23:465:817 PD3890a NCBI-37 8 65511900 - 8 65518362 - 2 TG 0 Ensembl58 intron5 intron4 CYP7B1 CYP7B1 ENSG00000172817 ENSG00000172817 ENST00000310193 ENST00000310193 -1 -1 9420 9420 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 EAS56_153:7:24:243:1772 PD3890a NCBI-37 8 72938448 - 8 72944779 - 2 CC 0 Ensembl58 intron24 intron23 TRPA1 TRPA1 ENSG00000104321 ENSG00000104321 ENST00000262209 ENST00000262209 -1 -1 8989 8989 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:3:3:1786:1168 PD3890a NCBI-37 8 80797896 - 8 80807336 - 1 C 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 12 4 EAS192_92:3:2:985:1759 PD3890a NCBI-37 8 94999695 - 8 95003999 - 4 ATCC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 EAS56_153:3:4:497:1437 PD3890a NCBI-37 8 95109911 - 8 95370355 - 1 G 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 21292447 PD3890a NCBI-37 9 88359109 + 12 11348642 - 4 AAAA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 EAS56_153:8:28:827:406 PD3890a NCBI-37 9 112186842 - 9 112192243 - 3 GGG 0 Ensembl58 intron12 intron10 PTPN3 PTPN3 ENSG00000070159 ENSG00000070159 ENST00000374541 ENST00000374541 -1 -1 5774 5774 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 EAS56_153:3:17:1333:708 PD3890a NCBI-37 9 14129728 - 9 14192453 - 0 2 AA Ensembl58 intron6 intron2 NFIB NFIB ENSG00000147862 ENSG00000147862 ENST00000380959 ENST00000380959 -1 -1 4781 4781 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS56_153:8:37:797:1240 PD3890a NCBI-37 9 15917119 + 9 15922067 + 2 AA 0 Ensembl58 intron24 intron25 C9orf93 C9orf93 ENSG00000164989 ENSG00000164989 ENST00000380701 ENST00000380701 1 1 203238 203238 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 EAS56_153:3:18:391:815 PD3890a NCBI-37 X 29734830 - X 29738117 - 5 TGACT 0 Ensembl58 intron5 intron5 IL1RAPL1 IL1RAPL1 ENSG00000169306 ENSG00000169306 ENST00000302196 ENST00000302196 1 1 11141 11141 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 EAS192_92:2:75:414:976 PD3890a NCBI-37 X 2974522 - X 2986470 - 1 C 0 Ensembl58 intron1 intron2 ARSF ARSF ENSG00000062096 ENSG00000062096 ENST00000381127 ENST00000381127 1 1 416 416 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL12_3375:5:79:1778:998 PD3904a NCBI-37 1 108202927 - 1 108361444 - 2 GA 0 Ensembl58 intron19 intron2 VAV3 VAV3 ENSG00000134215 ENSG00000134215 ENST00000370056 ENST00000370056 -1 -1 10451 10451 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 13 4 IL25_3353:5:32:1689:1203 PD3904a NCBI-37 1 181600397 + 1 181601713 + 2 AG 0 Ensembl58 intron6 intron6 CACNA1E CACNA1E ENSG00000198216 ENSG00000198216 ENST00000367570 ENST00000367570 1 1 777 777 deletion somatic MAQ-0.7.1 capillary_sequencing 11 2 IL12_3375:2:116:1507:1362 PD3904a NCBI-37 1 186866548 + 1 186867452 + 3 AAG 0 Ensembl58 intron5 intron5 PLA2G4A PLA2G4A ENSG00000116711 ENSG00000116711 ENST00000367466 ENST00000367466 1 1 5321 5321 deletion somatic MAQ-0.7.1 capillary_sequencing 9 2 34117210 PD3904a NCBI-37 1 199665701 - 1 211638877 - 5 TTTTT 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 12 4 IL12_3375:1:40:361:1506 PD3904a NCBI-37 1 22122727 + 1 22135788 + 15 CTCCTGCCTCAGCCT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL12_3375:6:53:966:9 PD3904a NCBI-37 10 22299562 - 10 92039304 - 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 34637427 PD3904a NCBI-37 10 45309268 + 10 65796572 + 1 A 0 Ensembl58 intron7 ENSG00000224812 ENSG00000226426 ENSG00000224812 ENSG00000226426 ENST00000450287 ENST00000451946 -1 -1 deletion somatic BWA-0.5.8 BRASS-0 36 2 34644570/IL12_3375:3:85:1478:1823 PD3904a NCBI-37 10 80845494 - 10 97184496 - 2 TG 0 Ensembl58 intron1 intron6 ZMIZ1 SORBS1 ENSG00000108175 ENSG00000095637 ENST00000334512 ENST00000371247 1 -1 57178 10580 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 43 13 4 34646324 PD3904a NCBI-37 10 86881323 + 10 93404461 - 2 TG 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 25 1 34646491/IL12_3375:3:51:818:1583 PD3904a NCBI-37 10 88234900 - 10 89330503 + 3 CAA 0 Ensembl58 intron4 intergenic WAPAL ENSG00000062650 ENST00000298767 -1 23063 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 19 6 8 IL12_3375:3:51:47:1771 PD3904a NCBI-37 10 88405861 + 10 93244056 + 1 T 0 Ensembl58 intergenic intron8 HECTD2 ENSG00000165338 ENST00000298068 1 143279 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 34647367 PD3904a NCBI-37 10 93404505 + 10 96921260 + 0 33 GATGCTCTCTTCAGAGCCAGCATGGAGGAACAT Ensembl58 intergenic intron1 ENSG00000231829 ENSG00000231829 ENST00000422744 -1 deletion somatic BWA-0.5.8 BRASS-0 45 2 34648205 PD3904a NCBI-37 10 99127608 + 17 36792904 + 50 GCTCACTGCAACCTCCACCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGC 0 Ensembl58 intron23 intergenic RRP12 ENSG00000052749 ENST00000414986 -1 23223 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL12_3375:6:91:883:1959 PD3904a NCBI-37 11 26605328 + 11 26606181 + 2 AA 0 Ensembl58 intron14 intron14 ANO3 ANO3 ENSG00000134343 ENSG00000134343 ENST00000256737 ENST00000256737 1 1 63982 63982 deletion somatic MAQ-0.7.1 capillary_sequencing 16 2 34672938/IL12_3375:3:6:9:560 PD3904a NCBI-37 11 65888421 - 11 76944290 - 1 G 0 Ensembl58 intron1 intron12 PACS1 GDPD4 ENSG00000175115 ENSG00000178795 ENST00000320580 ENST00000315938 1 -1 55690 220032 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 66 23 4 34673402/IL12_3375:6:91:942:614 PD3904a NCBI-37 11 67511155 + 11 76800547 + 0 0 Ensembl58 intergenic intron2 CAPN5 ENSG00000149260 ENST00000278559 1 726 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 78 8 2 34673972 PD3904a NCBI-37 11 67874075 - 11 73792023 - 3 CAG 0 Ensembl58 intron1 intron22 CHKA C2CD3 ENSG00000110721 ENSG00000168014 ENST00000356135 ENST00000313663 -1 -1 1119 26005 amplicon_associated somatic BWA-0.5.8 BRASS-0 33 4 IL12_3375:3:32:494:1120 PD3904a NCBI-37 11 70056931 + 11 70220557 + 1 T 0 Ensembl58 intergenic intron23 PPFIA1 ENSG00000131626 ENST00000389547 1 8500 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 23 2 34675961/IL12_3375:7:120:827:701 PD3904a NCBI-37 11 75299989 + 11 76800291 - 6 TCCTGA 0 Ensembl58 intron3 intron2 MAP6 CAPN5 ENSG00000171533 ENSG00000149260 ENST00000304771 ENST00000278559 -1 1 4135 726 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 75 22 1 IL12_3375:2:80:1654:1497 PD3904a NCBI-37 11 76765699 - 11 76810904 + 0 7 CTGAGAC Ensembl58 intergenic intron3 CAPN5 ENSG00000149260 ENST00000278559 1 726 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 16 8 34676577 PD3904a NCBI-37 11 79995447 + 18 13193801 + 2 TT 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 91 32 IL12_3375:5:116:1110:1163 PD3904a NCBI-37 12 104116524 - 12 127640816 + 2 GC 0 Ensembl58 intron44 intergenic STAB2 ENSG00000136011 ENST00000388887 1 55576 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 6 8 IL12_3375:5:116:1201:887 PD3904a NCBI-37 12 112170704 + 12 112173003 + 2 CT 0 Ensembl58 intron10 intron11 ACAD10 ACAD10 ENSG00000111271 ENSG00000111271 ENST00000313698 ENST00000313698 1 1 80724 80724 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL25_3353:7:24:341:1615 PD3904a NCBI-37 12 13536846 + 12 13550301 + 1 G 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL12_3375:3:19:573:41 PD3904a NCBI-37 12 49459564 + 12 49466962 + 4 AGCT 0 Ensembl58 intron6 intergenic RHEBL1 ENSG00000167550 ENST00000301068 -1 121268 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL12_3375:8:94:550:1297 PD3904a NCBI-37 12 119962912 + 17 61383185 - 3 CTT 0 Ensembl58 intron11 intron7 CCDC60 TANC2 ENSG00000183273 ENSG00000170921 ENST00000327554 ENST00000424789 1 1 160777 26115 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL25_3353:7:66:360:411 PD3904a NCBI-37 13 48058664 + 13 48060803 + 2 TT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 9 2 34715848/IL19_3558:3:14:1380:814 PD3904a NCBI-37 13 54977262 - 13 67760274 - 1 G 0 Ensembl58 intergenic intron1 PCDH9 ENSG00000184226 ENST00000328454 -1 5101 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 18 5 4 34715984/IL12_3375:8:89:379:1335 PD3904a NCBI-37 13 55971528 + 13 67772053 + 0 0 Ensembl58 intergenic intron1 PCDH9 ENSG00000184226 ENST00000328454 -1 5101 deletion somatic MAQ-0.7.1 capillary_sequencing 12 6 2 34715985 PD3904a NCBI-37 13 55971790 - 13 58585611 + 3 TGA 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 34 8 34715991 PD3904a NCBI-37 13 55972983 + 13 67754364 + 3 TGT 0 Ensembl58 intergenic intron1 PCDH9 ENSG00000184226 ENST00000328454 -1 5101 deletion somatic BWA-0.5.8 BRASS-0 49 2 34716488/IL19_3558:3:114:852:1423 PD3904a NCBI-37 13 59594413 + 13 60920928 - 1 T 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 33 7 1 IL12_3375:3:88:645:1158 PD3904a NCBI-37 13 95914337 - 18 52313461 + 18 CATGTTGCCCTAGGCTGG 0 Ensembl58 intron1 intergenic ABCC4 ENSG00000125257 ENST00000431522 -1 10257 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 18 32 IL25_3353:7:62:626:888 PD3904a NCBI-37 14 21573324 + 14 21584291 + 3 TTG 0 Ensembl58 intergenic intron1 ENSG00000178107 ENSG00000178107 ENST00000320322 1 deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 IL12_3375:5:17:741:673 PD3904a NCBI-37 14 58681548 + 14 58682661 + 0 0 Ensembl58 intron6 intron7 ACTR10 ACTR10 ENSG00000131966 ENSG00000131966 ENST00000254286 ENST00000254286 1 1 55860 55860 deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 34741229/IL25_3353:1:53:1782:1859 PD3904a NCBI-37 15 27615153 + 15 32303812 + 4 TGCT 0 Ensembl58 intron5 intergenic GABRG3 ENSG00000182256 ENST00000333743 1 2567 deletion somatic MAQ-0.7.1 capillary_sequencing 16 3 2 IL19_3558:3:38:117:1389 PD3904a NCBI-37 15 59168346 + 15 59177945 + 0 2 CA Ensembl58 intergenic intron19 SLTM ENSG00000137776 ENST00000380516 -1 79811 deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 IL12_3375:5:95:83:998 PD3904a NCBI-37 15 71729204 + 15 71730082 + 2 CA 0 Ensembl58 intron6 intron6 THSD4 THSD4 ENSG00000187720 ENSG00000187720 ENST00000261862 ENST00000261862 1 1 79875 79875 deletion somatic MAQ-0.7.1 capillary_sequencing 10 2 IL25_3353:1:101:1194:1549 PD3904a NCBI-37 16 30648735 + 16 30655138 + 2 AG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL12_3375:3:118:359:502 PD3904a NCBI-37 17 47678958 - 17 47793993 - 2 GA 0 Ensembl58 intron9 intron6 SPOP FAM117A ENSG00000121067 ENSG00000121104 ENST00000393331 ENST00000240364 -1 -1 8405 81558 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 10 4 34784558/IL12_3375:3:113:1150:887 PD3904a NCBI-37 18 40942478 + 18 41711260 + 0 3 TGC Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 35 19 2 34780144 PD3904a NCBI-37 18 5855023 + 18 8003282 + 3 TAC 0 Ensembl58 intergenic intron7 PTPRM ENSG00000173482 ENST00000332175 1 5797 deletion somatic BWA-0.5.8 BRASS-0 20 2 IL25_3353:5:106:589:1602 PD3904a NCBI-37 19 14482131 + 19 14484950 + 0 1 G Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL12_3375:3:93:1540:1947 PD3904a NCBI-37 19 21903056 + 19 21905574 + 5 GTTAT 0 Ensembl58 intron5 intergenic ENSG00000249576 ENSG00000249576 ENST00000504760 1 deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 34139632 PD3904a NCBI-37 2 10003868 - 2 20609341 - 0 47 CTGTATTCAGGAAACCCATCTCACATGCAGAGACACACATAGGCTCA Ensembl58 intron5 intergenic TAF1B ENSG00000115750 ENST00000263663 1 9014 tandem_duplication somatic BWA-0.5.8 BRASS-0 21 4 IL25_3353:7:61:689:312 PD3904a NCBI-37 2 178879703 + 2 178880411 + 3 CTA 0 Ensembl58 intron2 intron2 PDE11A PDE11A ENSG00000128655 ENSG00000128655 ENST00000450799 ENST00000450799 -1 -1 50940 50940 deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 IL25_3353:1:10:807:507 PD3904a NCBI-37 21 33085131 + 21 33092106 + 0 34 CTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC Ensembl58 intron1 intron1 SFRS15 SFRS15 ENSG00000156304 ENSG00000156304 ENST00000399804 ENST00000399804 -1 -1 57466 57466 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL12_3375:3:112:907:1037 PD3904a NCBI-37 3 113623955 - 3 113628975 + 0 0 Ensembl58 intron8 intron9 GRAMD1C GRAMD1C ENSG00000178075 ENSG00000178075 ENST00000358160 ENST00000358160 1 1 54762 54762 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 2 8 IL12_3375:5:89:1508:928 PD3904a NCBI-37 3 113624426 + 3 114111021 - 0 9 ATATTTTAA Ensembl58 intron8 intron6 GRAMD1C ZBTB20 ENSG00000178075 ENSG00000181722 ENST00000358160 ENST00000357258 1 -1 54762 26137 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 IL12_3375:6:113:812:1050 PD3904a NCBI-37 3 134650762 + 3 134652618 + 0 6 ATATAT Ensembl58 intron2 intron2 EPHB1 EPHB1 ENSG00000154928 ENSG00000154928 ENST00000398015 ENST00000398015 1 1 2047 2047 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL19_3558:3:6:1008:2034 PD3904a NCBI-37 3 159605899 + 3 159606609 + 0 3 TAG Ensembl58 intron5 exon6 SCHIP1 SCHIP1 ENSG00000151967 ENSG00000151967 ENST00000486290 ENST00000486290 1 1 29970 29970 deletion somatic MAQ-0.7.1 capillary_sequencing 9 2 IL25_3353:3:114:1440:1960 PD3904a NCBI-37 3 163744409 + 3 163749268 + 0 1 T Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL12_3375:3:24:1331:1374 PD3904a NCBI-37 3 185060280 + 3 185086634 + 2 AG 0 Ensembl58 intron2 intron2 MAP3K13 MAP3K13 ENSG00000073803 ENSG00000073803 ENST00000424227 ENST00000424227 1 1 9175 9175 deletion somatic MAQ-0.7.1 capillary_sequencing 10 2 IL12_3375:6:21:1311:1331 PD3904a NCBI-37 3 195995359 + 3 195995922 + 4 GCAA 0 Ensembl58 intron2 intron2 PCYT1A PCYT1A ENSG00000161217 ENSG00000161217 ENST00000431016 ENST00000431016 -1 -1 5130 5130 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 34248521/IL12_3375:1:1:40:867 PD3904a NCBI-37 3 18943200 + X 10186127 + 2 CA 0 Ensembl58 intron6 intron11 ENSG00000233386 CLCN4 ENSG00000233386 ENSG00000073464 ENST00000425799 ENST00000380833 1 1 1183 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 21 10 32 IL12_3375:1:58:1235:1384 PD3904a NCBI-37 4 132168687 + 4 132170313 + 3 GTA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 2 2 IL12_3375:3:18:882:506 PD3904a NCBI-37 4 160096221 + 4 160098093 + 3 GTG 0 Ensembl58 intron1 intron1 RAPGEF2 RAPGEF2 ENSG00000109756 ENSG00000109756 ENST00000505478 ENST00000505478 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 10 2 IL25_3353:1:110:505:1110 PD3904a NCBI-37 4 47552535 + 4 47553206 + 1 C 0 Ensembl58 intron10 intron10 ATP10D ATP10D ENSG00000145246 ENSG00000145246 ENST00000273859 ENST00000273859 1 1 57205 57205 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL25_3353:2:20:1583:754 PD3904a NCBI-37 4 80887164 + 4 80920450 - 0 41 CCCACTGTTGTGGGGTGGGGGGAGGGGGGAAGGATAGTGTT Ensembl58 intron16 intron12 ANTXR2 ANTXR2 ENSG00000163297 ENSG00000163297 ENST00000403729 ENST00000403729 -1 -1 118429 118429 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL12_3375:7:93:1275:1719 PD3904a NCBI-37 4 47005891 + X 7057700 + 0 256 TCAGGATGGAAATGTTCTGTAACTATACTGCATCCGATGGGAGCCACAGCTGGAAACCGGGTTCATGAGACGTGACTCATGCAACTGAGGACCTGAATTTCTCGTGTTATTTAAATAGCCCCCAATGACTAATTGCCAAAACGTAACATAGAGACACAAAATATAGAGTGGACAGCACAACTCCAGAGGAATGCATTCACTCATCCTTAATCTATTTAGAAAATACTCTGCTGGGTGTTACAAAGGCTTCAAAATT Ensembl58 intron1 intron1 GABRB1 HDHD1A ENSG00000163288 ENSG00000130021 ENST00000513567 ENST00000424830 1 -1 8226 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 32 34410658/IL12_3375:3:7:1053:35 PD3904a NCBI-37 5 53675579 + 17 36727793 + 1 T 0 Ensembl58 intergenic intron2 SRCIN1 ENSG00000017373 ENST00000264659 -1 80725 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 19 8 32 34430098/IL12_3375:6:19:63:1264 PD3904a NCBI-37 5 141623605 + 18 48598261 + 2 CT 0 Ensembl58 intergenic intron9 SMAD4 ENSG00000141646 ENST00000398417 1 4089 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 59 18 32 IL19_3558:3:117:707:263 PD3904a NCBI-37 5 155082038 + 5 155083001 + 3 TTC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 30 2 IL19_3558:3:20:1782:330 PD3904a NCBI-37 5 165933336 + 5 165933938 + 3 CTT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 11 2 IL25_3353:3:90:1166:875 PD3904a NCBI-37 5 165962407 - 5 173627023 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL12_3375:5:15:241:1209 PD3904a NCBI-37 5 165968010 + 5 173638665 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 10 1 34435766/IL12_3375:7:9:1249:1364 PD3904a NCBI-37 5 167536271 + 5 169454265 + 2 GA 0 Ensembl58 intron7 intron33 ODZ2 DOCK2 ENSG00000145934 ENSG00000134516 ENST00000403607 ENST00000256935 1 1 57451 1794 deletion somatic MAQ-0.7.1 capillary_sequencing 47 17 2 IL12_3375:5:18:214:680 PD3904a NCBI-37 5 169874366 - 5 173022381 + 5 AGAGG 0 Ensembl58 intron1 intergenic KCNIP1 ENSG00000182132 ENST00000377360 1 30820 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 23 8 IL12_3375:5:32:919:1931 PD3904a NCBI-37 5 170044135 + 5 173638377 + 0 1 A Ensembl58 intron1 intergenic KCNIP1 ENSG00000182132 ENST00000411494 1 30820 deletion somatic MAQ-0.7.1 capillary_sequencing 13 2 IL25_3353:7:67:1391:1167 PD3904a NCBI-37 5 38538642 + 5 38539299 + 0 4 CAAA Ensembl58 intron1 intron1 LIFR LIFR ENSG00000113594 ENSG00000113594 ENST00000263409 ENST00000263409 -1 -1 3977 3977 deletion somatic MAQ-0.7.1 capillary_sequencing 13 2 IL12_3375:3:82:629:250 PD3904a NCBI-37 6 24717603 - 17 20032443 + 0 4 TGTT Ensembl58 intron1 intron3 C6orf62 CYTSB ENSG00000112308 ENSG00000128487 ENST00000378119 ENST00000261503 -1 1 81688 92521 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL12_3375:6:30:570:1175 PD3904a NCBI-37 6 24718043 + 6 24719777 + 0 2 TT Ensembl58 intron1 5UTR C6orf62 C6orf62 ENSG00000112308 ENSG00000112308 ENST00000378119 ENST00000378119 -1 -1 81688 81688 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 34460557 PD3904a NCBI-37 6 65175124 - 6 65460031 + 0 3 TTG Ensembl58 intron23 intron19 EYS EYS ENSG00000188107 ENSG00000188107 ENST00000370618 ENST00000370618 -1 -1 346007 346007 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 22 8 34460715 PD3904a NCBI-37 6 65560641 + 6 68525044 - 0 57 AAATTTACAATAAAATTATGTTGGTTGTCATCTAGCTATTTCAAAATAAATCATGTC Ensembl58 intron16 intergenic EYS ENSG00000188107 ENST00000370618 -1 346007 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 15 1 34460704/IL19_3558:3:102:770:239 PD3904a NCBI-37 6 65468796 + 8 39426816 - 0 0 Ensembl58 intron19 intergenic EYS ENSG00000188107 ENST00000370618 -1 346007 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 20 6 32 34486422 PD3904a NCBI-37 7 849238 - 15 49370508 + 3 GTA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 25 32 34556494/IL12_3375:8:12:507:111 PD3904a NCBI-37 8 63909052 - 11 37459528 - 0 3 CTG Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 51 21 32 34552489 PD3904a NCBI-37 8 48431887 - 15 25673316 - 0 42 GTAATCCGCCTGGGATTACAGGCGCATGCCACCATGCCCAAC Ensembl58 intron8 intron1 KIAA0146 UBE3A ENSG00000164808 ENSG00000114062 ENST00000297423 ENST00000232165 1 -1 23514 7337 interchromosomal somatic BWA-0.5.8 BRASS-0 27 32 IL25_3353:5:73:1222:680 PD3904a NCBI-37 8 31466395 - 8 37194304 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 8 IL12_3375:6:20:6:1091 PD3904a NCBI-37 8 31466514 + 8 38419252 + 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 19 2 34549281 PD3904a NCBI-37 8 31471822 - 8 38431245 - 4 CAAT 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 117 4 IL19_3558:3:10:1703:767 PD3904a NCBI-37 8 31472758 + 8 37183148 - 2 AA 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 34 1 IL12_3375:3:45:861:532 PD3904a NCBI-37 8 32251934 + 8 42160112 + 0 0 Ensembl58 intron1 intron5 NRG1 IKBKB ENSG00000157168 ENSG00000104365 ENST00000405606 ENST00000342222 1 1 3084 3551 deletion somatic MAQ-0.7.1 capillary_sequencing 11 2 34549867/IL12_3375:5:104:711:898 PD3904a NCBI-37 8 35047959 + 8 36891482 + 6 AAACAC 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 51 22 2 IL12_3375:5:45:330:838 PD3904a NCBI-37 8 36894486 - 8 37413602 + 0 14 CAGGGGTCTCAGGA Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 41 8 34550154/IL25_3353:5:63:1087:24 PD3904a NCBI-37 8 37164567 - 8 39072359 + 1 T 0 Ensembl58 intergenic intron12 ADAM32 ENSG00000197140 ENST00000379907 1 203102 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 144 43 8 IL12_3375:8:111:1670:747 PD3904a NCBI-37 8 37730235 - 8 39092774 - 0 0 Ensembl58 intron3 intron16 RAB11FIP1 ADAM32 ENSG00000156675 ENSG00000197140 ENST00000287263 ENST00000379907 -1 1 80223 203102 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 4 IL12_3375:7:70:791:1949 PD3904a NCBI-37 8 37944607 + 8 72378555 + 0 1 C Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 2 IL12_3375:5:6:559:1253 PD3904a NCBI-37 8 38419232 + 8 39104078 - 1 G 0 Ensembl58 intergenic intron17 ADAM32 ENSG00000197140 ENST00000379907 1 203102 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 24 1 34550789 PD3904a NCBI-37 8 39695119 + 8 61680356 + 1 T 0 Ensembl58 intron1 intron2 ADAM2 CHD7 ENSG00000104755 ENSG00000171316 ENST00000265708 ENST00000423902 -1 1 2515 55636 deletion somatic BWA-0.5.8 BRASS-0 18 2 34550885/IL25_3353:5:66:475:1851 PD3904a NCBI-37 8 39953246 - 8 63349185 + 5 GAAAT 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 26 11 8 34551180/IL19_3558:3:91:1746:1629 PD3904a NCBI-37 8 40927533 + 8 42311932 - 2 AA 0 Ensembl58 intergenic intron5 SLC20A2 ENSG00000168575 ENST00000342228 -1 6575 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 27 3 1 34551281 PD3904a NCBI-37 8 41197955 - 8 52917231 + 2 CA 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 47 8 IL12_3375:6:47:1286:1105 PD3904a NCBI-37 8 41375880 + 8 62273627 - 0 2 TA Ensembl58 intergenic intron2 CLVS1 ENSG00000177182 ENST00000325897 1 157807 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 IL12_3375:7:1:1565:855 PD3904a NCBI-37 8 50498256 - 8 51577601 + 2 TA 0 Ensembl58 intergenic intron13 SNTG1 ENSG00000147481 ENST00000338349 1 54212 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 6 8 IL12_3375:8:94:638:388 PD3904a NCBI-37 8 50498707 - 8 51577428 - 2 TC 0 Ensembl58 intergenic intron13 SNTG1 ENSG00000147481 ENST00000338349 1 54212 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 34554403 PD3904a NCBI-37 8 56364794 + 8 59074078 + 0 64 ACCTGCCTCATGACGTCACCTAACCCTAATTACCTCCCAAGTTTCCATTTTCAAATACAAAATT Ensembl58 intron2 intergenic XKR4 ENSG00000206579 ENST00000327381 1 114786 deletion somatic BWA-0.5.8 BRASS-0 41 2 34555064 PD3904a NCBI-37 8 58460429 - 8 59496782 - 0 0 Ensembl58 intergenic intron30 NSMAF ENSG00000035681 ENST00000427130 -1 8439 tandem_duplication somatic BWA-0.5.8 BRASS-0 37 4 34556155/IL12_3375:1:98:999:716 PD3904a NCBI-37 8 62787102 + 8 64493864 - 0 66 AGGAATACTTTACAGTATTTGATGTGTTACAGATTTTCTCTGAGGTGTATTCCTTTTGCCTATGTT Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 26 3 1 IL12_3375:3:114:551:1877 PD3904a NCBI-37 8 63523494 + 8 72632911 + 2 GT 0 Ensembl58 intron2 intergenic NKAIN3 ENSG00000185942 ENST00000328472 1 286183 deletion somatic MAQ-0.7.1 capillary_sequencing 25 2 IL12_3375:6:4:9:1128 PD3904a NCBI-37 8 63565289 + 8 63591376 + 2 TG 0 Ensembl58 intron2 intron2 NKAIN3 NKAIN3 ENSG00000185942 ENSG00000185942 ENST00000328472 ENST00000328472 1 1 286183 286183 deletion somatic MAQ-0.7.1 capillary_sequencing 18 2 IL12_3375:3:92:619:477 PD3904a NCBI-37 8 63595810 - 8 63600475 - 1 C 0 Ensembl58 intron2 intron2 NKAIN3 NKAIN3 ENSG00000185942 ENSG00000185942 ENST00000328472 ENST00000328472 1 1 286183 286183 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 34556647/IL25_3353:6:70:88:1854 PD3904a NCBI-37 8 64480685 + 8 66794307 - 1 G 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 30 7 1 IL12_3375:6:93:583:1239 PD3904a NCBI-37 8 76765883 - 8 92438258 - 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 IL25_3353:5:51:1069:315 PD3904a NCBI-37 9 117525420 + 9 117534799 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 8 2 IL12_3375:7:94:1765:1101 PD3904a NCBI-37 9 2171950 + 9 2186679 + 2 CA 0 Ensembl58 intron29 intron32 SMARCA2 SMARCA2 ENSG00000080503 ENSG00000080503 ENST00000382203 ENST00000382203 1 1 6595 6595 deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 IL12_3375:7:28:737:1706 PD3904a NCBI-37 9 77442377 + 9 77453056 + 2 AT 0 Ensembl58 intron7 intron5 TRPM6 TRPM6 ENSG00000119121 ENSG00000119121 ENST00000360774 ENST00000360774 -1 -1 140803 140803 deletion somatic MAQ-0.7.1 capillary_sequencing 9 2 IL12_3375:1:106:1336:1762 PD3904a NCBI-37 X 150134301 + X 150139946 + 2 CA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL31_3399:5:11:1052:242 PD3905a NCBI-37 1 157956984 + 1 217311133 + 4 CCAA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL31_3399:8:51:337:1749 PD3905a NCBI-37 1 169297690 - 1 169312732 - 1 A 0 Ensembl58 intron1 intron1 NME7 NME7 ENSG00000143156 ENSG00000143156 ENST00000367811 ENST00000367811 -1 -1 29922 29922 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL8_3388:8:81:204:742 PD3905a NCBI-37 1 42610206 + 1 42651003 + 2 TC 0 Ensembl58 intergenic intron11 FOXJ3 ENSG00000198815 ENST00000361346 -1 22887 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL31_3399:5:12:1181:216 PD3905a NCBI-37 1 72240940 + 1 72263584 + 1 T 0 Ensembl58 intron3 intron2 NEGR1 NEGR1 ENSG00000172260 ENSG00000172260 ENST00000357731 ENST00000357731 -1 -1 257194 257194 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL8_3388:6:83:1059:1240 PD3905a NCBI-37 1 86588588 + 1 86637844 + 4 ATAA 0 Ensembl58 intron3 intergenic COL24A1 ENSG00000171502 ENST00000370571 -1 255631 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL24_3142:5:17:1347:1837 PD3905a NCBI-37 1 191491920 + 22 39711431 - 0 0 Ensembl58 intergenic exon5 SNORD43 ENSG00000100316 ENST00000216146 -1 653881 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL24_3142:5:24:41:1513 PD3905a NCBI-37 1 23944731 - 3 10206977 - 2 GT 0 Ensembl58 intron2 intron1 MDS2 IRAK2 ENSG00000197880 ENSG00000134070 ENST00000477916 ENST00000256458 1 1 3656 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL8_3388:2:2:1240:1081 PD3905a NCBI-37 1 25624304 + 4 152749822 - 2 GT 0 Ensembl58 intron3 intergenic RHD ENSG00000187010 ENST00000328664 1 6007 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL8_3388:5:65:515:975 PD3905a NCBI-37 10 131044068 - 10 131059620 - 5 TTTTT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 34657444 PD3905a NCBI-37 10 101711388 + 13 59649477 - 44 TGGAGTCAAAGGAGATCATTTTGGAGCTTTAAGATTTGACTGCC 0 Ensembl58 intron4 intergenic DNMBP ENSG00000107554 ENST00000324109 -1 23268 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL24_3142:5:92:1437:1021 PD3905a NCBI-37 11 2593872 + 11 2615447 - 2 AG 0 Ensembl58 intron5 intron10 KCNQ1 KCNQ1 ENSG00000053918 ENSG00000053918 ENST00000155840 ENST00000155840 1 1 3784 3784 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL31_3399:7:55:1725:1720 PD3905a NCBI-37 11 28765905 + 11 28785819 + 2 AT 0 Ensembl58 intron2 intron2 ENSG00000249867 ENSG00000249867 ENSG00000249867 ENSG00000249867 ENST00000513853 ENST00000513853 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL31_3399:6:44:1368:680 PD3905a NCBI-37 11 38329033 - 11 38335756 - 2 AG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 34718847/IL8_3388:5:72:358:324 PD3905a NCBI-37 12 44887157 + 12 52152699 + 0 76 GTGATCTGCCCGCCTCGCCCTCCCAACGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTGTATTCTTAAT Ensembl58 intergenic intron14 SCN8A ENSG00000196876 ENST00000354534 1 6334 deletion somatic MAQ-0.7.1 capillary_sequencing 13 7 2 IL8_3388:2:116:1768:400 PD3905a NCBI-37 12 53139433 + 12 53142892 - 3 ATG 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 16 1 IL31_3399:2:84:1325:1501 PD3905a NCBI-37 12 44481767 - 15 59205657 + 2 TT 0 Ensembl58 intron3 intron4 TMEM117 SLTM ENSG00000139173 ENSG00000137776 ENST00000266534 ENST00000380516 1 -1 84216 79811 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 34720351 PD3905a NCBI-37 12 52198358 + X 46081448 - 58 TCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAACCTC 0 Ensembl58 intron26 intergenic SCN8A ENSG00000196876 ENST00000354534 1 6334 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL31_3399:1:114:31:708 PD3905a NCBI-37 13 70418592 - X 155110559 + 1 A 0 Ensembl58 intron5 intergenic KLHL1 ENSG00000150361 ENST00000377844 -1 57626 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 34764296 PD3905a NCBI-37 14 40882887 - 17 67210375 + 0 1 G Ensembl58 intergenic intron10 ABCA10 ENSG00000154263 ENST00000269081 -1 10349 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL31_3399:8:102:1406:1235 PD3905a NCBI-37 15 96602496 - 15 96606759 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL8_3388:8:74:814:986 PD3905a NCBI-37 17 75484932 - 17 75488462 - 2 CG 0 Ensembl58 exon7 intron8 Sep-09 Sep-09 ENSG00000184640 ENSG00000184640 ENST00000427177 ENST00000427177 1 1 10801 10801 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL31_3399:3:57:1223:1392 PD3905a NCBI-37 18 26063737 - 18 26071951 - 2 GG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 12 4 IL24_3142:5:26:70:952 PD3905a NCBI-37 18 45353254 - 18 46133982 - 1 T 0 Ensembl58 intergenic intron2 KIAA0427 ENSG00000134030 ENST00000382998 1 9811 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL31_3399:7:112:1693:512 PD3905a NCBI-37 2 74777499 + 11 46279794 + 5 GGGAC 0 Ensembl58 intron2 intergenic LOXL3 ENSG00000115318 ENST00000264094 -1 84695 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 32 33970360 PD3905a NCBI-37 2 7354929 + 19 6694988 + 0 0 Ensembl58 intron9 intron23 ENSG00000234603 C3 ENSG00000234603 ENSG00000125730 ENST00000441133 ENST00000245907 1 -1 718 interchromosomal somatic BWA-0.5.8 BRASS-0 9 32 IL8_3388:7:60:657:873 PD3905a NCBI-37 2 104480907 - 2 104487181 - 2 CA 0 Ensembl58 intron1 intron1 ENSG00000232597 ENSG00000232597 ENSG00000232597 ENSG00000232597 ENST00000455716 ENST00000455716 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL8_3388:6:101:900:1286 PD3905a NCBI-37 2 131592327 - 2 131602097 - 1 C 0 Ensembl58 intron1 intron1 ENSG00000233221 ARHGEF4 ENSG00000233221 ENSG00000136002 ENST00000429282 ENST00000409359 -1 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 34024646 PD3905a NCBI-37 2 180461418 - 2 186601459 - 1 G 0 Ensembl58 intron1 intron1 ZNF385B ENSG00000226747 ENSG00000144331 ENSG00000226747 ENST00000409343 ENST00000427269 -1 -1 151126 tandem_duplication somatic BWA-0.5.8 BRASS-0 11 4 IL31_3399:6:30:208:729 PD3905a NCBI-37 2 32012617 - 2 32018722 - 1 T 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 33986137 PD3905a NCBI-37 2 80536131 + 22 46624351 + 53 TGGTGGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACT 0 Ensembl58 intron11 intron6 CTNNA2 PPARA ENSG00000066032 ENSG00000186951 ENST00000466387 ENST00000407236 1 1 1496 5465 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 33983242 PD3905a NCBI-37 2 69175129 - 6 29354273 + 18 CTCGGCCTCCCAAAGTGC 0 Ensembl58 intron3 intron1 GKN2 OR12D3 ENSG00000183607 ENSG00000112462 ENST00000328895 ENST00000377143 -1 -1 200504 81797 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 33979117/IL8_3388:1:118:14:807 PD3905a NCBI-37 2 54059082 - 8 123912390 + 1 G 0 Ensembl58 intron1 intron2 ASB3 ZHX2 ENSG00000115239 ENSG00000178764 ENST00000406625 ENST00000314393 -1 1 51130 22882 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 10 6 32 IL31_3399:2:63:215:674 PD3905a NCBI-37 20 61538255 - X 94060977 - 3 TAA 0 Ensembl58 intron5 intergenic DIDO1 ENSG00000101191 ENST00000354665 -1 11083 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 34156300 PD3905a NCBI-37 3 185665068 + 11 126366154 - 2 TG 0 Ensembl58 intergenic intron3 KIRREL3 ENSG00000149571 ENST00000416561 -1 84623 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL31_3399:2:65:1105:1217 PD3905a NCBI-37 3 137344239 - 3 137349279 - 3 CAA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 34144653 PD3905a NCBI-37 3 156121901 - 3 186880405 - 0 21 TTAAACAAAAAACTAATATTA Ensembl58 intron1 intron2 KCNAB1 RPL39L ENSG00000169282 ENSG00000163923 ENST00000490337 ENST00000433055 1 -1 7881 116832 tandem_duplication somatic BWA-0.5.8 BRASS-0 12 4 IL31_3399:8:119:467:1648 PD3905a NCBI-37 3 64279495 + 3 64314823 - 1 T 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 8 1 IL31_3399:3:117:556:965 PD3905a NCBI-37 3 99069576 - 3 99074065 - 3 GCA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL31_3399:7:13:349:846 PD3905a NCBI-37 3 99698103 - 3 99705724 + 3 CAA 0 Ensembl58 intron1 intron1 FILIP1L C3orf26 ENSG00000168386 ENSG00000184220 ENST00000354552 ENST00000421999 -1 1 11259 84319 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 15 8 34152176 PD3905a NCBI-37 3 175247625 + 5 32292032 - 38 GTAGTCTTGGCAGAAGCATTGTGTGCAGGATAGGCAAA 0 Ensembl58 intron9 intron1 NAALADL2 MTMR12 ENSG00000177694 ENSG00000150712 ENST00000454872 ENST00000382142 1 -1 254827 54545 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 34120282 PD3905a NCBI-37 3 109773948 + 6 45476670 - 0 0 Ensembl58 intergenic intron4 ENSG00000250096 ENSG00000250096 ENST00000352853 1 860 interchromosomal somatic BWA-0.5.8 BRASS-0 32 32 IL31_3399:6:46:587:707 PD3905a NCBI-37 3 178539234 + 6 21333626 + 3 ACC 0 Ensembl58 intron1 intergenic KCNMB2 ENSG00000197584 ENST00000358316 1 10242 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 9 32 34166246 PD3905a NCBI-37 4 6425033 + 6 702906 + 54 GAGTGCAGTGGTGCAATCTCGGCTCACTGCAACCTCTGCCTCCCGGATTCAAGC 0 Ensembl58 intron1 intron6 PPP2R2C ENSG00000237960 ENSG00000074211 ENSG00000237960 ENST00000382599 ENST00000449432 -1 1 5522 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL31_3399:7:82:1329:609 PD3905a NCBI-37 5 107082347 - 5 107085558 - 2 TC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 IL31_3399:2:100:560:1750 PD3905a NCBI-37 5 177997148 - 5 178119478 - 4 ACAG 0 Ensembl58 intron1 intron2 COL23A1 ENSG00000249299 ENSG00000050767 ENSG00000249299 ENST00000390654 ENST00000503510 -1 -1 91522 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 IL31_3399:1:104:1312:1755 PD3905a NCBI-37 5 50686015 - 5 50689481 + 3 GAG 0 Ensembl58 intron4 3UTR ISL1 ISL1 ENSG00000016082 ENSG00000016082 ENST00000230658 ENST00000230658 1 1 3670 3670 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 8 8 IL24_3142:5:81:886:933 PD3905a NCBI-37 5 71400379 - 5 71417613 - 2 CT 0 Ensembl58 intergenic intron2 MAP1B ENSG00000131711 ENST00000296755 1 4131 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 34332496 PD3905a NCBI-37 5 173140210 + 6 39661136 - 3 GTT 0 Ensembl58 intergenic intron3 KIF6 ENSG00000164627 ENST00000287152 -1 221458 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 34321240/IL31_3399:6:15:402:923 PD3905a NCBI-37 5 139929508 - 9 78726777 - 4 GCAC 0 Ensembl58 intergenic intron9 PCSK5 ENSG00000099139 ENST00000376752 1 5125 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 3 32 IL31_3399:7:22:1563:516 PD3905a NCBI-37 6 136948399 - 6 136966222 - 1 T 0 Ensembl58 intron14 intron11 MAP3K5 MAP3K5 ENSG00000197442 ENSG00000197442 ENST00000359015 ENST00000359015 -1 -1 4217 4217 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 IL8_3388:1:80:1388:179 PD3905a NCBI-37 6 141717180 - 6 141720459 - 1 A 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL31_3399:2:49:1063:763 PD3905a NCBI-37 6 20506212 - 6 20512228 - 1 A 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL31_3399:8:88:1646:121 PD3905a NCBI-37 6 21342237 + 6 55261251 - 0 0 Ensembl58 intergenic intron6 GFRAL ENSG00000187871 ENST00000340465 1 389400 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 2 1 34358403 PD3905a NCBI-37 6 33712052 + 6 35249466 + 0 0 Ensembl58 intron1 intron2 IP6K3 ZNF76 ENSG00000161896 ENSG00000065029 ENST00000451316 ENST00000373953 -1 1 117283 7629 deletion somatic BWA-0.5.8 BRASS-0 4 2 IL31_3399:2:95:405:904 PD3905a NCBI-37 6 3435217 + 6 3623815 + 0 0 Ensembl58 intron1 intron2 SLC22A23 ENSG00000228793 ENSG00000137266 ENSG00000228793 ENST00000380302 ENST00000443445 -1 -1 63027 deletion somatic MAQ-0.7.1 capillary_sequencing 13 2 IL31_3399:3:95:21:1585 PD3905a NCBI-37 6 9212604 - 6 42215708 + 0 7 TACCATA Ensembl58 intergenic intron13 TRERF1 ENSG00000124496 ENST00000372922 -1 55809 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 34350205 PD3905a NCBI-37 6 23391138 + 7 41271050 + 1 T 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 34426201 PD3905a NCBI-37 7 7272350 + 10 118780671 - 38 GTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGA 0 Ensembl58 intron1 intergenic C1GALT1 ENSG00000106392 ENST00000436587 1 56913 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 34434927 PD3905a NCBI-37 7 31196605 + 12 114009989 + 48 GTCTTTGAGGAATCACCACACTGTCTTCCACAATGGTTGAACTAATTT 0 Ensembl58 intron1 intergenic ENSG00000251425 ENSG00000251425 ENST00000507825 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 34430835/IL24_3142:5:85:770:514 PD3905a NCBI-37 7 19538790 + 18 54813771 - 2 AG 0 Ensembl58 intron4 intergenic ENSG00000223838 ENSG00000223838 ENST00000412563 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 15 6 32 34435514/IL31_3399:5:53:993:1810 PD3905a NCBI-37 7 32681407 - 7 33440718 - 1 T 0 Ensembl58 intron10 intron18 AVL9 BBS9 ENSG00000105778 ENSG00000122507 ENST00000404479 ENST00000355070 1 1 27241 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 10 4 4 IL8_3388:1:116:1224:1718 PD3905a NCBI-37 7 50903663 - 7 50924045 - 6 GGCAGC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL8_3388:3:15:58:979 PD3905a NCBI-37 7 52443702 - 7 52451842 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 34479993/IL31_3399:1:80:748:1776 PD3905a NCBI-37 7 95973689 + 7 116210582 + 2 CA 0 Ensembl58 intergenic intron1 ENSG00000243220 ENSG00000243220 ENST00000421965 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 11 7 2 34553430 PD3905a NCBI-37 8 110687749 - 11 90751659 + 63 TTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCTTCTGTATTTTCTAGTTTAT 0 Ensembl58 intron1 intergenic ENSG00000147642 ENSG00000147642 ENST00000422135 -1 55638 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 34558672 PD3905a NCBI-37 8 123289989 + 11 4584960 + 50 GCCAAATCATGAATGAACTCCCATTCACAATTGCTACAAAGAGAATAAAA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL31_3399:8:37:1721:1196 PD3905a NCBI-37 8 109713553 + 8 109715927 + 2 GC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL31_3399:6:113:416:863 PD3905a NCBI-37 8 120606320 - 8 121375175 - 2 AG 0 Ensembl58 intron12 intron45 ENPP2 COL14A1 ENSG00000136960 ENSG00000187955 ENST00000259486 ENST00000297848 -1 1 5168 7373 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL8_3388:1:120:1750:455 PD3905a NCBI-37 8 141470497 - 8 143439230 - 4 ATCC 0 Ensembl58 intergenic intron1 TSNARE1 ENSG00000171045 ENST00000307180 -1 203062 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 34578122 PD3905a NCBI-37 9 28182632 - 10 23576725 - 50 GTAAATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTTGCCCACTTTT 0 Ensembl58 intron4 intron7 LINGO2 C10orf67 ENSG00000174482 ENSG00000179133 ENST00000379992 ENST00000376500 -1 -1 158038 interchromosomal somatic BWA-0.5.8 BRASS-0 2 32 IL31_3399:2:57:1626:1780 PD3905a NCBI-37 9 15200078 + 9 73225822 - 1 T 0 Ensembl58 intron7 intron17 TTC39B TRPM3 ENSG00000155158 ENSG00000083067 ENST00000355694 ENST00000377110 -1 -1 158219 80036 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 34578168/IL31_3399:1:64:1631:1297 PD3905a NCBI-37 9 28314917 - 9 77018999 + 0 13 GTAATAATAACTG Ensembl58 intron3 intergenic LINGO2 ENSG00000174482 ENST00000308675 -1 158038 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 4 8 IL31_3399:3:12:19:1448 PD3905a NCBI-37 9 83574770 + 9 83670396 + 2 GA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL8_3388:2:93:80:1770 PD3905a NCBI-37 9 93652971 - 9 127568190 + 4 CTGA 0 Ensembl58 intron13 intron6 SYK OLFML2A ENSG00000165025 ENSG00000185585 ENST00000375746 ENST00000373580 1 1 6850 169611 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 6 8 24065907/IL14_4765:5:41:19777:13526 PD3945a NCBI-37 1 219832829 + 12 59759863 + 2 TT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 28 6 32 24539571 PD3945a NCBI-37 10 29105642 + 12 24210086 + 2 AA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL14_4765:2:51:5455:3416 PD3945a NCBI-37 13 91425126 + 13 91426785 + 0 2 CT Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL14_4765:5:112:19477:19006 PD3945a NCBI-37 13 26473763 + 17 20750672 + 2 AG 0 Ensembl58 intron33 intergenic ATP8A2 ENSG00000132932 ENST00000381655 1 51761 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL14_4765:2:7:11816:16427 PD3945a NCBI-37 14 83828507 + 14 83829354 + 3 TCA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 24706170 PD3945a NCBI-37 18 65421202 - 19 19159917 + 0 1 T Ensembl58 intron1 intron3 ENSG00000246923 ARMC6 ENSG00000246923 ENSG00000105676 ENST00000500778 ENST00000269932 1 1 93436 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 24095764 PD3945a NCBI-37 2 69554984 - 2 70626823 - 4 TCTG 0 Ensembl58 intron17 intergenic GFPT1 ENSG00000198380 ENST00000361060 -1 2673 tandem_duplication somatic BWA-0.5.8 BRASS-0 4 4 IL14_4765:5:17:4981:2804 PD3945a NCBI-37 20 43961670 - 20 44111689 - 2 CA 0 Ensembl58 exon3 intergenic SDC4 ENSG00000124145 ENST00000372733 -1 6385 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 24746473 PD3945a NCBI-37 22 35674583 + 22 49531957 + 0 0 Ensembl58 intron4 intergenic HMGXB4 ENSG00000100281 ENST00000444518 1 10042 deletion somatic BWA-0.5.8 BRASS-0 6 2 IL14_4765:4:73:8692:14969 PD3945a NCBI-37 5 61861479 + 12 54809247 + 3 CAT 0 Ensembl58 intron27 intron1 IPO11 ITGA5 ENSG00000086200 ENSG00000161638 ENST00000409296 ENST00000293379 1 -1 51194 3678 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 24379273 PD3945a NCBI-37 7 55520507 + 10 112550424 + 6 TTTGTT 0 Ensembl58 intron4 intron5 VOPP1 RBM20 ENSG00000154978 ENSG00000203867 ENST00000462326 ENST00000369519 -1 1 282996 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 24376896 PD3945a NCBI-37 7 48626147 + 7 97334398 - 0 1 T Ensembl58 intron56 intergenic ABCA13 ENSG00000179869 ENST00000435803 1 154664 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 9 1 24423791 PD3945a NCBI-37 8 32393216 - 8 51472607 + 4 AAAA 0 Ensembl58 intron1 intron10 NRG1 SNTG1 ENSG00000157168 ENSG00000147481 ENST00000405606 ENST00000338349 1 1 3084 54212 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 4 8 IL14_4765:5:34:11676:19285 PD3945a NCBI-37 8 35713188 + 8 58655593 - 0 216 CGCCAGCAAAGACTAACAAAAAGGTCTAGATCTTTCTTCCCCTTCGATGAGTGAGGGCTTCTCTTGTTGTGCCTGCCCCATGTTTACCCACCGGGATTGAGAATGCTCCTCCCTTCGGTTGCGAAAAGTAGCACAAGNAGTACGCGTCCCCCTCTGCGGGCATGTTCTCTTTCGCCCCCCACCCGTAAAAAATTCCTTTCTCACACTTGGAAAAAA Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 30235167 PD4005a NCBI-37 11 99311546 + 12 7252039 - 3 AAA 0 Ensembl58 intergenic intron5 C1RL ENSG00000139178 ENST00000266542 -1 51279 interchromosomal somatic BWA-0.5.8 BRASS-0 9 32 29847948 PD4005a NCBI-37 6 168321281 - 11 13100691 + 0 0 Ensembl58 intron19 intergenic ENSG00000249273 ENSG00000249273 ENST00000466024 1 4301 interchromosomal somatic BWA-0.5.8 BRASS-0 20 32 IL33_4608:5:112:18279:19494 PD4006a NCBI-37 1 157625020 - 1 159236640 + 0 17 TTTATCTTTACACCTCT Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:3:109:12791:3657 PD4006a NCBI-37 1 183551714 - 1 183555988 - 2 GA 0 Ensembl58 intron2 intron2 NCF2 NCF2 ENSG00000116701 ENSG00000116701 ENST00000367535 ENST00000367535 -1 -1 4688 4688 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:5:62:10911:7158 PD4006a NCBI-37 1 185786978 + 1 185791480 + 0 25 TTGTAGAGCACAAAAAGCTGTTTCG Ensembl58 intron1 intron1 HMCN1 HMCN1 ENSG00000143341 ENSG00000143341 ENST00000271588 ENST00000271588 1 1 83872 83872 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL33_4608:5:95:18680:4121 PD4006a NCBI-37 1 218748497 - 1 218983744 - 3 TGC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:3:119:11468:5783 PD4006a NCBI-37 1 234643136 + 1 234813869 + 2 CA 0 Ensembl58 intergenic intron1 ENSG00000228044 ENSG00000228044 ENST00000453568 1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL33_4608:5:15:17623:5491 PD4006a NCBI-37 1 23665443 - 1 23711586 - 1 G 0 Ensembl58 intron2 intron9 HNRNPR TCEA3 ENSG00000125944 ENSG00000204219 ENST00000374612 ENST00000450454 -1 -1 10236 6920 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:5:17:12091:15475 PD4006a NCBI-37 1 92840743 - 1 92843838 - 3 TGC 0 Ensembl58 intron11 intron11 RPAP2 RPAP2 ENSG00000122484 ENSG00000122484 ENST00000370343 ENST00000370343 1 1 79871 79871 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 33612320 PD4006a NCBI-37 1 90432656 - 2 137060072 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL33_4608:1:114:3985:4299 PD4006a NCBI-37 1 41857261 - 22 42079609 + 1 C 0 Ensembl58 intergenic intron1 NHP2L1 ENSG00000100138 ENST00000401959 -1 4809 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL33_4608:5:58:15441:17528 PD4006a NCBI-37 1 41869761 + 22 42091678 - 3 TGA 0 Ensembl58 intergenic 3UTR C22orf46 ENSG00000184208 ENST00000402966 1 79640 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 32 IL33_4608:6:53:7432:16601 PD4006a NCBI-37 12 121014033 - 12 121019766 + 0 0 Ensembl58 intron16 intergenic RNF10 ENSG00000022840 ENST00000325954 1 9921 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:2:54:9703:12347 PD4006a NCBI-37 12 2900445 - 12 2912423 - 2 GC 0 Ensembl58 intergenic exon10 FKBP4 ENSG00000004478 ENST00000001008 1 2288 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL33_4608:6:102:14934:15795 PD4006a NCBI-37 12 3746127 + 12 3764954 + 0 4 CATC Ensembl58 intron14 intron9 EFCAB4B EFCAB4B ENSG00000130038 ENSG00000130038 ENST00000440314 ENST00000440314 -1 -1 84766 84766 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL33_4608:5:67:17691:12958 PD4006a NCBI-37 12 67702129 - 12 67703672 + 2 TA 0 Ensembl58 intron11 intron11 CAND1 CAND1 ENSG00000111530 ENSG00000111530 ENST00000299218 ENST00000299218 1 1 55832 55832 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 IL33_4608:3:109:6666:16080 PD4006a NCBI-37 12 99922404 + 12 100317458 + 0 4 ATTA Ensembl58 intron9 intron1 ANKS1B ANKS1B ENSG00000185046 ENSG00000185046 ENST00000329257 ENST00000329257 -1 -1 56899 56899 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL33_4608:2:119:11636:14903 PD4006a NCBI-37 13 31851096 + 14 65689635 + 3 AGA 0 Ensembl58 intron10 intergenic B3GALTL ENSG00000187676 ENST00000343307 1 145173 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL33_4608:2:37:4361:19237 PD4006a NCBI-37 14 86978997 + 14 87142039 + 1 T 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL33_4608:1:5:6243:15731 PD4006a NCBI-37 14 92210470 - 14 92617993 - 0 9 GTATATATT Ensembl58 intergenic intron9 CPSF2 ENSG00000165934 ENST00000298875 1 53981 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 34963222 PD4006a NCBI-37 15 25623831 + 15 56855884 + 0 0 Ensembl58 intron1 intergenic UBE3A ENSG00000114062 ENST00000438097 -1 7337 deletion somatic BWA-0.5.8 BRASS-0 8 2 IL33_4608:1:100:8803:11950 PD4006a NCBI-37 16 15133272 - 16 15146397 - 5 TTCTT 0 Ensembl58 intron8 intron1 NTAN1 NTAN1 ENSG00000157045 ENSG00000157045 ENST00000287706 ENST00000287706 -1 -1 123803 123803 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL33_4608:2:94:8726:6453 PD4006a NCBI-37 16 24086858 - 16 24089542 - 1 A 0 Ensembl58 intron5 intron5 PRKCB PRKCB ENSG00000166501 ENSG00000166501 ENST00000321728 ENST00000321728 1 1 5579 5579 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 34990666 PD4006a NCBI-37 17 44093025 - 17 46176285 - 0 17 TGTTTTTGTTTTGTTTT Ensembl58 intron13 intron1 MAPT CBX1 ENSG00000186868 ENSG00000108468 ENST00000344290 ENST00000225603 1 -1 4137 10951 tandem_duplication somatic BWA-0.5.8 BRASS-0 13 4 IL33_4608:6:75:18340:11548 PD4006a NCBI-37 17 32936625 - 18 37040034 + 3 CAT 0 Ensembl58 intron1 intron3 TMEM132E ENSG00000249862 ENSG00000181291 ENSG00000249862 ENST00000321639 ENST00000510201 1 -1 124842 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL33_4608:2:99:18071:8737 PD4006a NCBI-37 18 66483069 - 18 66486340 - 2 CT 0 Ensembl58 intron1 intron1 CCDC102B CCDC102B ENSG00000150636 ENSG00000150636 ENST00000319445 ENST00000319445 1 1 79839 79839 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:3:94:10884:16932 PD4006a NCBI-37 19 34593518 - 19 34606269 - 2 TA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 33759821 PD4006a NCBI-37 2 220380786 + 11 33520177 - 2 GC 0 Ensembl58 intron1 intergenic ACCN4 ENSG00000072182 ENST00000358078 1 55515 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 IL33_4608:1:116:9880:16524 PD4006a NCBI-37 2 43278893 - 2 43584594 - 3 ACT 0 Ensembl58 intergenic intron29 THADA ENSG00000115970 ENST00000405006 -1 63892 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL33_4608:5:82:13208:14090 PD4006a NCBI-37 2 55182346 + 2 55353254 + 3 GCA 0 Ensembl58 intron31 intergenic EML6 ENSG00000214595 ENST00000356458 1 400954 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 33710436 PD4006a NCBI-37 2 69339724 + 2 178231571 - 2 AA 0 Ensembl58 intron10 intron1 ANTXR1 NFE2L2 ENSG00000169604 ENSG00000116044 ENST00000409829 ENST00000464747 1 -1 84168 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 19 1 33724670 PD4006a NCBI-37 2 98892269 + 2 145322408 + 5 ATAAT 0 Ensembl58 intron22 intergenic VWA3B ENSG00000168658 ENST00000305068 1 200403 deletion somatic BWA-0.5.8 BRASS-0 15 2 IL33_4608:1:68:8731:15793 PD4006a NCBI-37 20 30937602 + 20 31019679 + 0 0 Ensembl58 intergenic intron10 ASXL1 ENSG00000171456 ENST00000375687 1 171023 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL33_4608:1:70:6859:4407 PD4006a NCBI-37 20 57071643 - 20 57084725 - 4 CCCT 0 Ensembl58 intron1 intron1 APCDD1L APCDD1L ENSG00000198768 ENSG00000198768 ENST00000371149 ENST00000371149 -1 -1 164284 164284 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:5:14:4302:5288 PD4006a NCBI-37 3 140679627 - 3 140705642 + 3 TTT 0 Ensembl58 intron3 intergenic SLC25A36 ENSG00000114120 ENST00000324194 1 55186 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:2:111:6339:9634 PD4006a NCBI-37 3 157654561 - 3 157872620 - 0 4 ATAA Ensembl58 intergenic intron3 RSRC1 ENSG00000174891 ENST00000295930 1 51319 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:1:90:15763:17549 PD4006a NCBI-37 3 15814257 - 3 15826793 - 0 2 AT Ensembl58 intron2 intron2 ANKRD28 ANKRD28 ENSG00000206560 ENSG00000206560 ENST00000412318 ENST00000412318 -1 -1 23243 23243 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL33_4608:3:111:7511:10840 PD4006a NCBI-37 3 179311645 - 3 179316562 + 0 2 TC Ensembl58 exon4 intron2 MRPL47 MRPL47 ENSG00000136522 ENSG00000136522 ENST00000392659 ENST00000392659 -1 -1 57129 57129 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL33_4608:2:117:12287:18926 PD4006a NCBI-37 3 42797166 - 3 42809254 - 0 100 GGTGATCCACCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACGCCTAGCCTAGTAAGTCTTAAGGTCAGGTAGTGTCAGTT Ensembl58 intron3 intron1 CCDC13 CCDC13 ENSG00000244607 ENSG00000244607 ENST00000310232 ENST00000310232 -1 -1 152206 152206 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 33825425 PD4006a NCBI-37 4 2368888 - 4 2689989 - 0 0 Ensembl58 intron1 intron11 ZFYVE28 FAM193A ENSG00000159733 ENSG00000125386 ENST00000290974 ENST00000382839 -1 1 57732 8603 tandem_duplication somatic BWA-0.5.8 BRASS-0 7 4 IL33_4608:2:106:5543:17306 PD4006a NCBI-37 4 88975686 + 4 88979674 + 1 A 0 Ensembl58 intron7 intron9 PKD2 PKD2 ENSG00000118762 ENSG00000118762 ENST00000237596 ENST00000237596 1 1 5311 5311 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 33913929 PD4006a NCBI-37 5 67587611 - 16 74740421 - 0 0 Ensembl58 intron1 intergenic PIK3R1 ENSG00000145675 ENST00000336483 1 5295 interchromosomal somatic BWA-0.5.8 BRASS-0 19 32 IL33_4608:5:54:6505:2360 PD4006a NCBI-37 5 106772401 - 5 106806593 - 3 TTT 0 Ensembl58 intron1 intron1 EFNA5 EFNA5 ENSG00000184349 ENSG00000184349 ENST00000333274 ENST00000333274 -1 -1 1946 1946 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 33977706 PD4006a NCBI-37 6 27301759 - 12 57888546 + 0 19 GAACTGAAATGTGAACCCA Ensembl58 intergenic intron7 MARS ENSG00000166986 ENST00000262027 1 4141 interchromosomal somatic BWA-0.5.8 BRASS-0 9 32 IL33_4608:6:44:10454:5420 PD4006a NCBI-37 6 105124574 - 6 105128198 + 1 T 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL33_4608:2:10:12678:5652 PD4006a NCBI-37 6 106470775 - 6 106480862 - 2 TT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 IL33_4608:6:49:14412:14320 PD4006a NCBI-37 6 20959297 - 6 21169367 - 3 CTT 0 Ensembl58 intron8 intron11 CDKAL1 CDKAL1 ENSG00000145996 ENSG00000145996 ENST00000378610 ENST00000378610 1 1 54901 54901 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 33960849 PD4006a NCBI-37 6 3458435 - 6 145195686 + 0 4 CATA Ensembl58 intron1 intergenic ENSG00000247306 ENSG00000247306 ENST00000500936 1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 10 8 34005271/IL33_4608:2:60:15284:8898 PD4006a NCBI-37 6 72611771 - 6 135942069 - 2 CT 0 Ensembl58 intron1 intergenic RIMS1 ENSG00000079841 ENST00000264839 1 22999 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 12 4 4 33963733 PD4006a NCBI-37 6 7410709 - 6 7826557 - 6 CAAAGG 0 Ensembl58 intron13 intron1 RIOK1 BMP6 ENSG00000124784 ENSG00000153162 ENST00000379834 ENST00000283147 1 1 83732 654 tandem_duplication somatic BWA-0.5.8 BRASS-0 28 4 IL33_4608:3:40:16259:3317 PD4006a NCBI-37 7 110639518 - 7 110718353 - 3 CAC 0 Ensembl58 intron4 intron4 IMMP2L IMMP2L ENSG00000184903 ENSG00000184903 ENST00000331762 ENST00000331762 -1 -1 83943 83943 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL33_4608:1:83:14888:9382 PD4006a NCBI-37 7 117631103 - 7 117888374 - 0 2 AT Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:6:59:15084:2397 PD4006a NCBI-37 7 150858537 - 7 150867001 - 3 GAT 0 Ensembl58 intron1 intron1 GBX1 GBX1 ENSG00000164900 ENSG00000164900 ENST00000297537 ENST00000475831 -1 -1 2636 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 34416643 PD4006a NCBI-37 8 61762886 - 10 126862306 - 0 0 Ensembl58 intron25 intergenic CHD7 ENSG00000171316 ENST00000423902 1 55636 interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 34355605 PD4006a NCBI-37 8 3831172 + 8 4092285 + 1 C 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 8 2 IL33_4608:3:20:10848:14584 PD4006a NCBI-37 8 53226766 - 8 53229282 - 3 GAG 0 Ensembl58 intron2 intron2 ST18 ST18 ENSG00000147488 ENSG00000147488 ENST00000276480 ENST00000276480 -1 -1 9705 9705 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL33_4608:5:30:17705:5366 PD4006a NCBI-37 8 64704577 + 8 64766457 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL33_4608:3:65:11036:18525 PD4006a NCBI-37 8 84913464 + 8 84914532 + 0 4 GTCA Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL33_4608:3:39:10603:11225 PD4006a NCBI-37 9 14165219 - 9 14178125 - 7 TGGGAGA 0 Ensembl58 intron3 intron3 NFIB NFIB ENSG00000147862 ENSG00000147862 ENST00000380959 ENST00000380959 -1 -1 4781 4781 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL33_4608:3:44:14246:18106 PD4006a NCBI-37 X 21754873 - X 22001968 - 3 ACA 0 Ensembl58 intron4 intron7 SMPX SMS ENSG00000091482 ENSG00000102172 ENST00000379494 ENST00000404933 -1 1 23676 6611 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 24889632 PD4085a NCBI-37 1 101598272 - 1 107970986 + 1 T 0 Ensembl58 intergenic intron6 NTNG1 ENSG00000162631 ENST00000370066 1 22854 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 6 8 25756782 PD4085a NCBI-37 16 47786585 - 20 45733571 + 0 0 Ensembl58 intergenic intron9 EYA2 ENSG00000064655 ENST00000372063 1 2139 interchromosomal somatic BWA-0.5.8 BRASS-0 11 32 IL30_5011:2:37:7976:11104 PD4085a NCBI-37 16 47850304 + 20 38820046 + 2 GC 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 25050976 PD4085a NCBI-37 2 186145415 - 13 31481564 - 0 18 AGGTTTCGCACTTATTTA Ensembl58 intergenic intron1 C13orf33 ENSG00000102802 ENST00000380482 1 84935 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 25817621 PD4085a NCBI-37 20 24116037 - 20 54172631 - 0 81 AAGAAAGAAAAAGAACAGTGTGGAATATATGACAAAAAGTCCTGAATAATACCTTCGCAATGGAGATGAGGACTATTTCTG Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 9 4 IL30_5011:1:116:11516:2668 PD4085a NCBI-37 20 24144659 + 20 38864988 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 7 2 IL30_5011:1:116:17447:2904 PD4085a NCBI-37 5 105203334 + 5 128674671 - 1 G 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 2 1 25308977 PD4085a NCBI-37 5 112860255 + 5 114025413 + 0 0 Ensembl58 intron2 intron1 YTHDC2 ENSG00000246316 ENSG00000047188 ENSG00000246316 ENST00000161863 ENST00000498912 1 -1 64848 deletion somatic BWA-0.5.8 BRASS-0 8 2 IL30_5011:1:120:14840:19045 PD4085a NCBI-37 5 81925457 - 5 96132248 - 1 T 0 Ensembl58 intergenic intron4 ERAP1 ENSG00000164307 ENST00000443439 -1 51752 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL30_5011:1:92:2682:14797 PD4085a NCBI-37 5 95040315 + 5 111226411 - 0 0 Ensembl58 intron3 intron1 ENSG00000250240 C5orf13 ENSG00000250240 ENSG00000134986 ENST00000512486 ENST00000450761 -1 -1 9315 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 2 1 IL30_5011:2:89:13889:12757 PD4085a NCBI-37 5 96798223 - 5 129744311 - 3 TCT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 2 4 25278580 PD4085a NCBI-37 5 66119089 + 6 109736050 + 1 C 0 Ensembl58 intron3 intron6 MAST4 PPIL6 ENSG00000069020 ENSG00000185250 ENST00000406374 ENST00000447468 1 -1 375449 285755 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 25386451/IL30_5011:1:4:16545:10979 PD4085a NCBI-37 6 75573050 - 17 68079431 - 0 0 Ensembl58 intergenic intron1 KCNJ16 ENSG00000153822 ENST00000392671 1 3773 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 7 32 25389795 PD4085a NCBI-37 6 76535995 + 17 70412252 + 3 AGA 0 Ensembl58 intron3 intron3 MYO6 ENSG00000227036 ENSG00000196586 ENSG00000227036 ENST00000369977 ENST00000453722 1 -1 4646 interchromosomal somatic BWA-0.5.8 BRASS-0 41 32 IL7_4895:7:104:10530:4944 PD4086a NCBI-37 1 223458027 + 1 223461991 + 2 GG 0 Ensembl58 intron3 intron3 SUSD4 SUSD4 ENSG00000143502 ENSG00000143502 ENST00000366878 ENST00000366878 -1 -1 55061 55061 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 IL7_4895:5:88:4768:18047 PD4086a NCBI-37 10 126315686 - 10 136417439 - 0 0 Ensembl58 intron4 intergenic FAM53B ENSG00000189319 ENST00000337318 -1 9679 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL7_4895:7:101:5781:11119 PD4086a NCBI-37 10 5520388 - 10 5538443 + 1 G 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL7_4895:6:42:7041:4110 PD4086a NCBI-37 16 57810327 - 21 39130447 - 1 C 0 Ensembl58 intron2 intron2 KIFC3 KCNJ6 ENSG00000140859 ENSG00000157542 ENST00000421376 ENST00000400482 -1 -1 3801 3763 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL7_4895:8:28:8065:10352 PD4086a NCBI-37 18 293330 + 18 304282 + 0 1 G Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL7_4895:7:59:3014:7602 PD4086a NCBI-37 18 461333 + 18 464276 - 0 2 GT Ensembl58 intron2 intron2 COLEC12 COLEC12 ENSG00000158270 ENSG00000158270 ENST00000400256 ENST00000400256 -1 -1 81035 81035 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 11 1 IL7_4895:6:89:15882:4440 PD4086a NCBI-37 18 5515556 + 18 5527751 + 2 CA 0 Ensembl58 intron1 intron1 EPB41L3 EPB41L3 ENSG00000082397 ENSG00000082397 ENST00000341928 ENST00000341928 -1 -1 23136 23136 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL7_4895:8:110:15070:9120 PD4086a NCBI-37 20 30334810 + 20 30336162 - 3 CCT 0 Ensembl58 intron2 intron2 TPX2 TPX2 ENSG00000088325 ENSG00000088325 ENST00000300403 ENST00000300403 1 1 22974 22974 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 49 1 IL7_4895:8:37:11094:3879 PD4086a NCBI-37 20 49175740 - 20 49179438 - 4 ACAA 0 Ensembl58 intron1 intron2 PTPN1 PTPN1 ENSG00000196396 ENSG00000196396 ENST00000371621 ENST00000371621 1 1 5770 5770 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 IL7_4895:5:84:10165:14454 PD4086a NCBI-37 22 32276234 - 22 32427180 + 2 CA 0 Ensembl58 intron36 intergenic DEPDC5 ENSG00000100150 ENST00000400248 1 9681 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 9 4 IL7_4895:7:103:7635:3813 PD4086a NCBI-37 3 12630535 - 3 12808480 - 3 GCA 0 Ensembl58 intron12 intron1 RAF1 TMEM40 ENSG00000132155 ENSG00000088726 ENST00000251849 ENST00000264728 -1 -1 5894 55287 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL7_4895:6:94:12887:19156 PD4086a NCBI-37 4 54565874 + 4 54567804 + 33 ATTCAAGTTGGGATTTGGATGGGGACACAGCCA 0 Ensembl58 intron1 intron12 ENSG00000250443 FIP1L1 ENSG00000250443 ENSG00000145216 ENST00000511394 ENST00000507166 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 8 2 IL7_4895:6:22:2388:15320 PD4086a NCBI-37 5 123761207 + 5 123882374 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 27323327 PD4086a NCBI-37 6 3264061 - 6 3388385 + 1 G 0 Ensembl58 intron2 intron3 PSMG4 SLC22A23 ENSG00000180822 ENSG00000137266 ENST00000419065 ENST00000406686 1 -1 389362 63027 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 14 8 IL7_4895:8:71:13620:9913 PD4086a NCBI-37 6 76823800 - 6 76963283 - 2 TG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL7_4895:5:90:8185:7733 PD4086a NCBI-37 7 104041007 - 7 113660727 - 1 A 0 Ensembl58 intron1 intron1 LHFPL3 PPP1R3A ENSG00000187416 ENSG00000154415 ENST00000335925 ENST00000449795 1 -1 375612 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 27425952 PD4086a NCBI-37 7 105120966 + 7 111908290 + 0 0 Ensembl58 intron9 intron1 PUS7 ZNF277 ENSG00000091127 ENSG00000198839 ENST00000469408 ENST00000361822 -1 1 54517 11179 deletion somatic BWA-0.5.8 BRASS-0 11 2 27426065 PD4086a NCBI-37 7 105868154 - 7 127463714 + 2 AA 0 Ensembl58 intergenic intron11 SND1 ENSG00000197157 ENST00000354725 1 27044 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 14 8 IL7_4895:7:34:11192:5869 PD4086a NCBI-37 7 108137152 + 7 108582879 - 0 0 Ensembl58 exon8 intron1 PNPLA8 ENSG00000229603 ENSG00000135241 ENSG00000229603 ENST00000422087 ENST00000413406 -1 1 50640 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 27426949 PD4086a NCBI-37 7 108183521 - 7 117802567 + 2 GA 0 Ensembl58 intron1 intergenic PNPLA8 ENSG00000135241 ENST00000489738 -1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 10 8 IL7_4895:5:114:1688:4976 PD4086a NCBI-37 7 109344812 + 7 122174084 - 3 CCT 0 Ensembl58 intergenic intron8 CADPS2 ENSG00000081803 ENST00000412584 -1 93664 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 IL7_4895:5:55:13425:3069 PD4086a NCBI-37 8 128538428 - 8 128762060 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL7_4895:8:53:3959:3484 PD4086a NCBI-37 X 105807021 + X 105807808 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 27819487 PD4086a NCBI-37 X 131044529 - X 146823971 + 1 T 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 13 8 IL7_4895:7:106:6908:7381 PD4086a NCBI-37 X 60024 - X 62020 + 2 GG 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 24884217 PD4088a NCBI-37 1 152063989 - 1 155443273 - 1 T 0 Ensembl58 intergenic intron3 ASH1L ENSG00000116539 ENST00000392403 -1 55870 tandem_duplication somatic BWA-0.5.8 BRASS-0 15 4 24910190 PD4088a NCBI-37 1 218260539 + 1 220374451 + 0 0 Ensembl58 intergenic intron9 RAB3GAP2 ENSG00000118873 ENST00000358951 -1 25782 deletion somatic BWA-0.5.8 BRASS-0 8 2 24862046/IL34_4839:5:100:9865:14910 PD4088a NCBI-37 1 112828266 - 10 79047822 - 2 CC 0 Ensembl58 intron1 intron2 ENSG00000231246 KCNMA1 ENSG00000231246 ENSG00000156113 ENST00000427290 ENST00000286627 -1 -1 3778 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 4 32 IL34_4839:1:26:3537:16511 PD4088a NCBI-37 1 208517040 + 10 83204717 + 1 A 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 24907326 PD4088a NCBI-37 1 210348828 + 3 169600693 - 2 AA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 IL34_4839:3:33:7525:12661 PD4088a NCBI-37 10 61873902 - 14 48205561 - 0 0 Ensembl58 intron4 intergenic ANK3 ENSG00000151150 ENST00000355288 -1 288 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25486227 PD4088a NCBI-37 10 80326576 - 14 49740019 + 0 0 Ensembl58 intron1 intergenic ENSG00000230417 ENSG00000230417 ENST00000421324 1 interchromosomal somatic BWA-0.5.8 BRASS-0 15 32 25536386 PD4088a NCBI-37 12 14425319 + 12 18150623 + 0 17 TCTATAAGAGTTCCACC Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 8 2 25536392 PD4088a NCBI-37 12 14428772 + 12 18154327 + 2 GA 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 6 2 IL34_4839:5:91:5079:2675 PD4088a NCBI-37 12 15831322 + 12 25914051 - 0 1 A Ensembl58 intron3 intergenic EPS8 ENSG00000151491 ENST00000281172 -1 2059 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 9 1 IL34_4839:5:93:18430:5059 PD4088a NCBI-37 12 25913592 - 12 25928317 + 4 TCTC 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 25556076 PD4088a NCBI-37 12 68890364 - 12 77552339 + 2 TT 0 Ensembl58 intron1 intergenic ENSG00000251695 ENSG00000251695 ENST00000504589 1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 14 8 25556999/IL34_4839:2:115:3232:18558 PD4088a NCBI-37 12 72155987 + 12 77543820 - 1 A 0 Ensembl58 intron1 intergenic RAB21 ENSG00000080371 ENST00000261263 1 23011 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 13 3 1 25560359 PD4088a NCBI-37 12 84975858 + 21 41733330 - 0 0 Ensembl58 intergenic intron4 DSCAM ENSG00000171587 ENST00000400454 -1 1826 interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 IL34_4839:1:31:7205:15146 PD4088a NCBI-37 14 31353332 - 14 33396761 - 0 27 CTCAGAGCCTCGGGTTAACAGAAGTCC Ensembl58 intron8 intergenic COCH ENSG00000100473 ENST00000396618 1 1690 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 25696633 PD4088a NCBI-37 17 11642120 + 17 12333563 + 2 AC 0 Ensembl58 intron28 intergenic DNAH9 ENSG00000007174 ENST00000361801 1 1770 deletion somatic BWA-0.5.8 BRASS-0 11 2 25702644/IL34_4839:3:80:12094:10225 PD4088a NCBI-37 17 35889691 - 17 36725697 + 1 A 0 Ensembl58 intron19 intron2 SYNRG SRCIN1 ENSG00000006114 ENSG00000017373 ENST00000345615 ENST00000264659 -1 -1 80725 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 24 5 8 25703724 PD4088a NCBI-37 17 46825595 - 17 53140615 + 0 4 GTCT Ensembl58 intergenic intron12 STXBP4 ENSG00000166263 ENST00000376352 1 252983 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 27 8 25703732/IL34_4839:2:116:9199:8912 PD4088a NCBI-37 17 46868984 - 17 74462479 - 0 0 Ensembl58 intron1 intron4 TTLL6 AANAT ENSG00000170703 ENSG00000129673 ENST00000305326 ENST00000250615 -1 1 284076 15 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 37 8 4 IL34_4839:1:80:12698:7847 PD4088a NCBI-37 17 47098420 + 17 62035464 + 1 C 0 Ensembl58 intron2 intron12 IGF2BP1 SCN4A ENSG00000159217 ENSG00000007314 ENST00000290341 ENST00000435607 1 -1 10642 6329 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 11 2 IL34_4839:3:110:4107:7895 PD4088a NCBI-37 17 47391951 - 17 70988230 + 2 CA 0 Ensembl58 intron2 intron4 ZNF652 SLC39A11 ENSG00000198740 ENSG00000133195 ENST00000430262 ENST00000255559 -1 -1 22834 201266 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 8 IL34_4839:3:116:15869:9090 PD4088a NCBI-37 17 48435481 + 17 70942637 + 4 TGGC 0 Ensembl58 intron9 intron5 XYLT2 SLC39A11 ENSG00000015532 ENSG00000133195 ENST00000017003 ENST00000255559 1 -1 64132 201266 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 2 IL34_4839:2:119:18395:14523 PD4088a NCBI-37 17 49062487 - 17 51399978 + 0 0 Ensembl58 intron22 intergenic SPAG9 ENSG00000008294 ENST00000357122 -1 9043 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 8 IL34_4839:3:35:13329:6735 PD4088a NCBI-37 17 49989565 + 17 50198689 - 0 62 CCCTGTCTTAAAAAAACAAACGAAAACCCAAACTATCAGTGCTGCTCCCAACATCTGTCTGC Ensembl58 intron4 intron2 CA10 CA10 ENSG00000154975 ENSG00000154975 ENST00000285273 ENST00000285273 -1 -1 56934 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 1 IL34_4839:2:21:7990:1948 PD4088a NCBI-37 17 50440314 + 17 66221652 - 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 1 IL34_4839:1:31:10277:8167 PD4088a NCBI-37 17 50544433 + 17 53285384 + 3 ATT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 2 IL34_4839:5:94:11289:9095 PD4088a NCBI-37 17 53227901 - 17 72295099 - 0 0 Ensembl58 intron17 intron6 STXBP4 DNAI2 ENSG00000166263 ENSG00000171595 ENST00000376352 ENST00000311014 1 1 252983 64446 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 4 IL34_4839:1:110:15118:9342 PD4088a NCBI-37 17 53612684 + 17 68116388 - 0 0 Ensembl58 intron1 intron2 ENSG00000236319 KCNJ16 ENSG00000236319 ENSG00000153822 ENST00000455347 ENST00000392670 -1 1 3773 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 1 IL34_4839:3:112:3117:15476 PD4088a NCBI-37 17 54409649 + 17 65792590 + 1 A 0 Ensembl58 intron3 intergenic ANKFN1 ENSG00000153930 ENST00000318698 1 162282 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 2 25713016 PD4088a NCBI-37 17 55270247 - 17 74071235 + 1 C 0 Ensembl58 intergenic exon1 GALR2 ENSG00000182687 ENST00000329003 1 8811 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 11 8 IL34_4839:2:50:10326:10229 PD4088a NCBI-37 17 57549183 + 17 67767105 + 0 112 GTTCTACTCTGATTTTAGGTATTTCTTTTCTTCTGCTAGCTTTGTGGTTAGTTTTCTCTTCTTTTCCTATTTCCTCTAGGTGTGACTTCAGATTGTTAATTTGTGATATTTC Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 7 2 IL34_4839:2:70:13475:8019 PD4088a NCBI-37 17 57549361 - 17 57554997 + 4 TTGG 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 7 8 IL34_4839:1:8:15228:5777 PD4088a NCBI-37 17 57554921 + 17 67833859 + 2 AA 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 2 IL34_4839:3:115:1972:17425 PD4088a NCBI-37 17 57595968 + 17 58170690 + 0 152 GCGGAGAACTGGTCTGACCATAAATTTACCAGGGCCGGGTTTTTCCCCACCCTAATAGAGCCTGAGGGTACTGCAGGAGACCAGGATGTATTTCAGTCCTTAACTCAGCCGCATAGGATAGACATTCTCAGAGCAGTCTCAAATCTCCGAAA Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 2 IL34_4839:1:18:13933:9096 PD4088a NCBI-37 17 57597315 - 17 66061817 - 3 AGA 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 11 4 IL34_4839:5:119:2501:6243 PD4088a NCBI-37 17 59912855 - 17 71889241 - 0 0 Ensembl58 intron6 intergenic BRIP1 ENSG00000136492 ENST00000259008 -1 83990 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 15 4 25720643 PD4088a NCBI-37 17 60738997 - 17 68275990 - 1 A 0 Ensembl58 intron1 intergenic MRC2 ENSG00000011028 ENST00000303375 1 9902 tandem_duplication somatic BWA-0.5.8 BRASS-0 31 4 IL34_4839:2:88:18689:6781 PD4088a NCBI-37 17 60915701 - 17 73419166 - 0 21 CTTTTCTTTCTTTTTTTTTTG Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 9 4 IL34_4839:5:53:14370:7320 PD4088a NCBI-37 17 61639791 - 17 63223641 - 1 T 0 Ensembl58 intron14 3UTR KCNH6 RGS9 ENSG00000173826 ENSG00000108370 ENST00000392968 ENST00000262406 1 1 81033 8787 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 7 4 IL34_4839:3:114:11092:7464 PD4088a NCBI-37 17 62484715 + 17 67783988 + 1 T 0 Ensembl58 intron4 intergenic POLG2 ENSG00000136480 ENST00000322670 -1 11232 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 14 2 25725123 PD4088a NCBI-37 17 62575187 + 17 74422014 + 3 AAG 0 Ensembl58 intron8 intron1 SMURF2 UBE2O ENSG00000108854 ENSG00000175931 ENST00000262435 ENST00000319380 -1 -1 64750 63893 deletion somatic BWA-0.5.8 BRASS-0 57 2 IL34_4839:5:87:6612:10757 PD4088a NCBI-37 17 63275913 - 17 68967623 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 8 25725880/IL34_4839:1:78:5968:6119 PD4088a NCBI-37 17 64124621 + 17 77652358 + 0 0 Ensembl58 intron6 intergenic CCDC46 ENSG00000154240 ENST00000392769 -1 201134 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 12 5 2 IL34_4839:1:51:10371:16627 PD4088a NCBI-37 17 65915980 + 17 71263950 + 3 TGA 0 Ensembl58 intron14 intergenic BPTF ENSG00000171634 ENST00000335221 1 2186 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 10 2 25729159 PD4088a NCBI-37 17 66185598 - 17 70992601 + 0 0 Ensembl58 intergenic intron4 SLC39A11 ENSG00000133195 ENST00000255559 -1 201266 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 7 8 IL34_4839:5:7:2002:13609 PD4088a NCBI-37 17 67833905 + 17 68268900 - 2 AT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 9 1 25730129/IL34_4839:2:85:9916:18494 PD4088a NCBI-37 17 68964543 - 17 69729214 - 6 TTTGTT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 69 29 4 IL34_4839:5:96:18684:6407 PD4088a NCBI-37 17 71256978 - 17 72023197 + 6 ATAGGG 0 Ensembl58 intron2 intergenic CPSF4L ENSG00000187959 ENST00000344935 -1 642843 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 8 25697342/IL34_4839:1:10:2927:5435 PD4088a NCBI-37 17 16797450 - 18 44867063 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 3 32 IL34_4839:3:32:12924:13394 PD4088a NCBI-37 17 8128348 + 18 24893545 - 1 G 0 Ensembl58 3UTR intergenic C17orf68 ENSG00000178971 ENST00000315684 -1 80169 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25712192 PD4088a NCBI-37 17 54180883 - X 118848943 - 5 CCAAC 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 IL34_4839:2:102:8084:5650 PD4088a NCBI-37 17 61491637 - X 102467708 + 0 0 Ensembl58 intron22 intron1 TANC2 ENSG00000226623 ENSG00000170921 ENSG00000226623 ENST00000424789 ENST00000416953 1 -1 26115 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 32 IL34_4839:2:97:7482:7220 PD4088a NCBI-37 17 61521216 + X 106696360 + 0 0 Ensembl58 intron1 intergenic CYB561 ENSG00000008283 ENST00000392976 -1 1534 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL34_4839:2:9:10803:12617 PD4088a NCBI-37 17 61521232 - X 107090586 - 3 CAG 0 Ensembl58 intron1 intron2 CYB561 MID2 ENSG00000008283 ENSG00000080561 ENST00000392976 ENST00000262843 -1 1 1534 11043 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL34_4839:1:101:8450:17037 PD4088a NCBI-37 17 61538735 - X 109943565 + 1 G 0 Ensembl58 intergenic intron7 CHRDL1 ENSG00000101938 ENST00000218054 -1 91851 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 25731108/IL34_4839:3:23:11366:18087 PD4088a NCBI-37 17 70973544 - X 111922317 - 2 GT 0 Ensembl58 intron4 intron1 SLC39A11 LHFPL1 ENSG00000133195 ENSG00000182508 ENST00000255559 ENST00000371968 -1 -1 201266 340596 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 13 7 32 25738778 PD4088a NCBI-37 18 11196454 + 18 12698509 - 1 T 0 Ensembl58 intergenic intron4 CEP76 ENSG00000101624 ENST00000262127 -1 79959 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 10 1 25742911 PD4088a NCBI-37 18 22549140 - 18 23800359 + 1 T 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 9 8 25746796/IL34_4839:5:117:9358:17624 PD4088a NCBI-37 18 43222046 - 18 58146721 + 1 T 0 Ensembl58 intron8 intergenic SLC14A2 ENSG00000132874 ENST00000255226 1 8170 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 19 5 8 25779294/IL34_4839:5:102:4367:6702 PD4088a NCBI-37 21 32261145 + 21 41547998 + 3 AAA 0 Ensembl58 intergenic intron15 DSCAM ENSG00000171587 ENST00000400454 -1 1826 deletion somatic MAQ-0.7.1 capillary_sequencing 12 6 2 25779302 PD4088a NCBI-37 21 32320023 - 21 42344561 + 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 17 8 25096203 PD4088a NCBI-37 3 166528998 - 17 29085925 - 0 0 Ensembl58 intron3 ENSG00000231516 ENSG00000247185 ENSG00000231516 ENSG00000247185 ENST00000475330 ENST00000502024 1 1 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL34_4839:2:68:17209:14462 PD4088a NCBI-37 3 166723122 - 17 35152999 - 1 T 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 32 IL34_4839:1:101:5848:17544 PD4088a NCBI-37 3 167115492 + 17 35933721 - 4 ATAA 0 Ensembl58 intron1 intron8 ENSG00000241669 SYNRG ENSG00000241669 ENSG00000006114 ENST00000498413 ENST00000345615 1 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL34_4839:1:67:14972:4070 PD4088a NCBI-37 3 167164887 + 17 27782663 - 1 A 0 Ensembl58 intron7 intron2 SERPINI2 TAOK1 ENSG00000114204 ENSG00000160551 ENST00000264677 ENST00000261716 -1 1 5276 57551 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 9 32 25098834/IL34_4839:5:101:7995:10141 PD4088a NCBI-37 3 170441700 + 17 37051644 - 1 G 0 Ensembl58 intron3 intron3 CLDN11 LASP1 ENSG00000013297 ENSG00000002834 ENST00000486975 ENST00000435347 1 1 3927 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 34 8 32 IL34_4839:3:102:3130:13197 PD4088a NCBI-37 3 187629144 - 17 50197015 + 0 0 Ensembl58 intergenic intron1 CA10 ENSG00000154975 ENST00000451037 -1 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 25101183 PD4088a NCBI-37 3 187644845 - 17 38421919 + 0 0 Ensembl58 intergenic intron5 WIPF2 ENSG00000171475 ENST00000323571 1 147179 interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 IL34_4839:5:65:14525:10227 PD4088a NCBI-37 3 188071520 + 17 50146961 - 0 0 Ensembl58 intron2 intron3 LPP CA10 ENSG00000145012 ENSG00000154975 ENST00000312675 ENST00000285273 1 -1 4026 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_4839:3:3:3468:15569 PD4088a NCBI-37 3 191720048 - 17 49993722 - 0 0 Ensembl58 intergenic intron3 CA10 ENSG00000154975 ENST00000451037 -1 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_4839:3:114:1054:10807 PD4088a NCBI-37 3 191721276 + 17 50201057 + 2 AT 0 Ensembl58 intergenic intron1 CA10 ENSG00000154975 ENST00000451037 -1 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 32 IL34_4839:3:106:6761:20348 PD4088a NCBI-37 3 191800437 + 17 57627119 + 0 1 T Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 32 IL34_4839:3:36:5532:9889 PD4088a NCBI-37 3 166977090 - 3 167064830 - 0 0 Ensembl58 intron16 intron6 ZBBX ZBBX ENSG00000169064 ENSG00000169064 ENST00000392767 ENST00000392767 -1 -1 79740 79740 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL34_4839:1:61:15760:3399 PD4088a NCBI-37 3 167065133 + 3 167115590 + 2 AG 0 Ensembl58 intron6 intron1 ZBBX ENSG00000241669 ENSG00000169064 ENSG00000241669 ENST00000392767 ENST00000498413 -1 1 79740 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 25039582 PD4088a NCBI-37 3 16746836 + 3 84959120 + 0 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 11 2 IL34_4839:1:67:7349:5587 PD4088a NCBI-37 3 187622151 - 3 192216073 - 2 AC 0 Ensembl58 intergenic intron2 FGF12 ENSG00000114279 ENST00000450716 -1 2257 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL34_4839:5:18:4793:10873 PD4088a NCBI-37 3 187644868 + 3 192107810 - 1 A 0 Ensembl58 intergenic intron2 FGF12 ENSG00000114279 ENST00000450716 -1 2257 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 7 1 25101185 PD4088a NCBI-37 3 187693088 - 3 188406896 - 0 44 TTGAGCCTGGGGTCGGCCTGGCACCCAGCTATGGTAGTTAGCAA Ensembl58 intron1 intron6 ENSG00000224187 LPP ENSG00000224187 ENSG00000145012 ENST00000446091 ENST00000312675 -1 1 4026 tandem_duplication somatic BWA-0.5.8 BRASS-0 4 4 25038636 PD4088a NCBI-37 3 7933765 - 3 88198961 + 4 CCCA 0 Ensembl58 intergenic 5UTR CGGBP1 ENSG00000163320 ENST00000462901 -1 8545 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 7 8 IL34_4839:1:90:12697:7504 PD4088a NCBI-37 9 102574825 - 9 130958112 + 1 A 0 Ensembl58 intron1 intron1 ENSG00000237461 CIZ1 ENSG00000237461 ENSG00000148337 ENST00000427039 ENST00000372948 -1 -1 25792 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL34_4839:2:77:16759:12187 PD4088a NCBI-37 9 17517806 + 9 102675836 + 4 TTGG 0 Ensembl58 intergenic intron1 STX17 ENSG00000136874 ENST00000259400 1 55014 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL34_4839:2:36:14003:12872 PD4088a NCBI-37 9 17841674 + 9 18158254 - 4 ACCA 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 25444071 PD4088a NCBI-37 9 74354206 + 9 103134735 - 16 GAGAATTGCTTGAACC 0 Ensembl58 intron5 intron2 TMEM2 ENSG00000235953 ENSG00000135048 ENSG00000235953 ENST00000377044 ENST00000429562 -1 1 23670 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 11 1 25445094/IL34_4839:1:95:18512:16387 PD4088a NCBI-37 9 80135576 - 9 102364203 - 2 CC 0 Ensembl58 intron2 intron3 GNA14 ENSG00000237461 ENSG00000156049 ENSG00000237461 ENST00000341700 ENST00000427039 -1 -1 9630 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 16 3 4 25446884 PD4088a NCBI-37 9 86624898 + 9 88538529 + 1 T 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 15 2 25446887 PD4088a NCBI-37 9 86625513 - 9 94452968 - 1 T 0 Ensembl58 intergenic intron12 ROR2 ENSG00000169071 ENST00000375715 -1 tandem_duplication somatic BWA-0.5.8 BRASS-0 17 4 24938603 PD4103a NCBI-37 1 185602920 + 1 196374293 + 2 TT 0 Ensembl58 intergenic intron12 KCNT2 ENSG00000162687 ENST00000294725 -1 343450 deletion somatic BWA-0.5.8 BRASS-0 8 2 IL26_5048:4:32:13274:16681 PD4103a NCBI-37 10 12383592 - 10 17863870 - 0 0 Ensembl58 intergenic intron1 MRC1L1 ENSG00000183748 ENST00000331429 1 414308 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL26_5048:2:21:9027:16242 PD4103a NCBI-37 10 1342465 + 10 11487262 + 0 0 Ensembl58 intron3 intergenic ADARB2 ENSG00000185736 ENST00000381312 -1 105 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 25561284/IL26_5048:2:48:10859:14604 PD4103a NCBI-37 10 20551257 + 10 21971833 + 0 0 Ensembl58 intron13 intron12 PLXDC2 MLLT10 ENSG00000120594 ENSG00000078403 ENST00000377252 ENST00000377059 1 1 84898 8028 deletion somatic MAQ-0.7.1 capillary_sequencing 21 3 2 IL26_5048:3:57:8365:5052 PD4103a NCBI-37 10 21951862 - 10 25070228 + 5 CCACT 0 Ensembl58 intron8 intergenic MLLT10 ENSG00000078403 ENST00000377059 1 8028 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 7 8 25564252 PD4103a NCBI-37 10 24726165 - 10 27766969 - 4 ATGA 0 Ensembl58 intron3 intergenic KIAA1217 ENSG00000120549 ENST00000430453 1 56243 amplicon_associated somatic BWA-0.5.8 BRASS-0 22 4 IL26_5048:2:20:17339:8201 PD4103a NCBI-37 10 50756574 + 10 50758966 + 3 TGA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 19 2 IL26_5048:4:55:15188:8644 PD4103a NCBI-37 10 55321668 + 10 55467931 - 3 TGA 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 IL26_5048:3:105:19657:13290 PD4103a NCBI-37 10 7668665 + 10 7783899 - 1 A 0 Ensembl58 intron5 intron16 ITIH5 ITIH2 ENSG00000123243 ENSG00000151655 ENST00000256861 ENST00000358415 -1 1 80760 3698 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 IL26_5048:3:47:6329:4233 PD4103a NCBI-37 10 800475 + 10 4301182 - 1 A 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 25552776/IL26_5048:4:47:1575:7962 PD4103a NCBI-37 10 8726801 - 10 28134397 + 0 0 Ensembl58 intergenic intron19 ARMC4 ENSG00000169126 ENST00000305242 -1 55130 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 26 6 8 IL26_5048:1:107:2750:8094 PD4103a NCBI-37 10 22307449 - 11 80875163 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 25584723/IL26_5048:3:62:4825:6082 PD4103a NCBI-37 10 50805157 + 11 74640532 + 4 CCTG 0 Ensembl58 intergenic intron6 XRRA1 ENSG00000166435 ENST00000321448 -1 143570 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 69 4 32 25584790 PD4103a NCBI-37 10 50957260 - 11 77760435 - 0 13 GCCTTCTAGGTTG Ensembl58 intron6 intergenic OGDHL ENSG00000197444 ENST00000432695 -1 55753 amplicon_associated somatic BWA-0.5.8 BRASS-0 8 32 IL26_5048:4:77:1502:18843 PD4103a NCBI-37 10 51101392 + 11 85353631 + 2 TA 0 Ensembl58 intron3 intergenic PARG ENSG00000227345 ENST00000402038 -1 8505 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 25585689/IL26_5048:2:38:10273:9474 PD4103a NCBI-37 10 55003841 - 11 80893330 - 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 273 36 32 IL26_5048:2:9:15564:13738 PD4103a NCBI-37 10 55007857 - 11 74924578 - 0 9 ATTAGCCAG Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 13 32 IL26_5048:3:7:14511:12179 PD4103a NCBI-37 10 55009693 + 11 80883032 - 1 C 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 36 32 IL26_5048:1:28:15749:6266 PD4103a NCBI-37 10 55573444 - 11 70345548 + 0 0 Ensembl58 intron33 intron30 PCDH15 SHANK2 ENSG00000150275 ENSG00000162105 ENST00000395438 ENST00000423696 -1 -1 65217 22941 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 25586472 PD4103a NCBI-37 10 55874147 - 11 69487357 + 0 0 Ensembl58 intron15 intron2 PCDH15 ORAOV1 ENSG00000150275 ENSG00000149716 ENST00000395438 ENST00000279147 -1 -1 65217 220064 amplicon_associated somatic BWA-0.5.8 BRASS-0 11 32 25586837/IL26_5048:4:11:19350:4420 PD4103a NCBI-37 10 56426725 + 11 69977708 + 0 0 Ensembl58 intron1 intron10 PCDH15 ANO1 ENSG00000150275 ENSG00000131620 ENST00000395438 ENST00000355303 -1 1 65217 55107 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 45 10 32 25591652/IL26_5048:2:117:11320:1214 PD4103a NCBI-37 10 57412037 + 11 74624856 + 0 0 Ensembl58 intergenic intron8 XRRA1 ENSG00000166435 ENST00000321448 -1 143570 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 537 72 32 IL26_5048:1:12:17145:16370 PD4103a NCBI-37 10 50758933 + 12 67875609 + 0 2 GG Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 32 25584638 PD4103a NCBI-37 10 50759837 + 12 64670672 - 0 97 ACAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCTTTATTTCCTTCTCCTGCCTAATTGCCCTGGCCAGAACTTCCAACACTATGTTGAAT Ensembl58 intergenic intron7 C12orf56 ENSG00000185306 ENST00000333722 -1 115749 amplicon_associated somatic BWA-0.5.8 BRASS-0 7 32 IL26_5048:1:58:7545:12602 PD4103a NCBI-37 10 55294232 - 12 67863888 + 2 AT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:3:79:2752:17559 PD4103a NCBI-37 10 57048085 + 12 109580609 + 0 31 CACATAGCAAAGTCAGGTAATTACCTGACTT Ensembl58 intron2 intron1 PCDH15 ACACB ENSG00000150275 ENSG00000076555 ENST00000373957 ENST00000377848 -1 1 32 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:2:114:16013:3988 PD4103a NCBI-37 10 57175104 - 12 66790944 + 0 0 Ensembl58 intron2 intron15 PCDH15 GRIP1 ENSG00000150275 ENSG00000155974 ENST00000373957 ENST00000398016 -1 -1 23426 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:2:3:8185:8458 PD4103a NCBI-37 10 57287051 - 17 8490107 - 1 T 0 Ensembl58 intron2 intron4 PCDH15 MYH10 ENSG00000150275 ENSG00000133026 ENST00000373957 ENST00000269243 -1 -1 4628 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 25555563 PD4103a NCBI-37 10 13061079 - X 95703080 + 15 CCCGGCTAATTTTTT 0 Ensembl58 intron5 intergenic CCDC3 ENSG00000151468 ENST00000378839 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 25626569/IL26_5048:1:43:8636:12104 PD4103a NCBI-37 11 66056634 - 11 76252012 + 0 0 Ensembl58 intergenic intron17 C11orf30 ENSG00000158636 ENST00000334736 1 56946 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 127 29 8 25628637 PD4103a NCBI-37 11 66107795 + 11 80439986 + 0 35 GCTGTTTGGTAAGTGCTGGGTTTGAATTAAGGACT Ensembl58 intron6 intergenic BRMS1 ENSG00000174744 ENST00000359957 -1 25855 amplicon_associated somatic BWA-0.5.8 BRASS-0 32 2 25629201 PD4103a NCBI-37 11 66418976 - 11 74924576 - 2 GT 0 Ensembl58 intron2 intergenic RBM4 ENSG00000173933 ENST00000396053 1 amplicon_associated somatic BWA-0.5.8 BRASS-0 22 4 25630142/IL26_5048:3:75:18738:16085 PD4103a NCBI-37 11 68005610 + 11 79967033 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 102 17 2 25630154 PD4103a NCBI-37 11 68007375 + 11 79487082 - 0 2 AA Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 5 1 25630357 PD4103a NCBI-37 11 68846673 - 11 79902818 - 0 0 Ensembl58 intron16 intergenic TPCN2 ENSG00000162341 ENST00000294309 1 219931 amplicon_associated somatic BWA-0.5.8 BRASS-0 165 4 IL26_5048:4:87:10131:17001 PD4103a NCBI-37 11 69418768 + 11 69420276 - 2 CC 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 10 1 25635921/IL26_5048:2:51:18081:11785 PD4103a NCBI-37 11 77285055 - 11 79616586 + 0 18 TTGGAGGCTGTATTAGAA Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 48 5 8 25636322/IL26_5048:3:85:15579:12909 PD4103a NCBI-37 11 79901976 - 11 80474251 + 1 C 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 213 40 8 25638733/IL26_5048:3:92:12959:21124 PD4103a NCBI-37 11 85355193 + 11 86141651 - 3 TAA 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 33 6 1 IL26_5048:1:119:14321:2930 PD4103a NCBI-37 11 69049625 + 12 70881129 - 0 0 Ensembl58 intergenic intron1 ENSG00000246966 ENSG00000246966 ENST00000501222 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:2:31:17042:5953 PD4103a NCBI-37 11 69602888 - 12 64170722 + 1 C 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL26_5048:1:26:3361:1649 PD4103a NCBI-37 11 74026667 - 12 70841203 - 0 9 TATGATGGC Ensembl58 intron3 intergenic ENSG00000246211 ENSG00000246211 ENST00000502071 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL26_5048:3:73:9826:16103 PD4103a NCBI-37 11 76718693 + 12 69722689 - 1 A 0 Ensembl58 intron7 intergenic ACER3 ENSG00000078124 ENST00000278544 1 55331 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25635882/IL26_5048:1:90:14128:15092 PD4103a NCBI-37 11 77093019 + 12 72218700 - 7 TGCCTTT 0 Ensembl58 intron2 intergenic PAK1 ENSG00000149269 ENST00000278568 -1 5058 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 30 4 32 IL26_5048:4:116:14191:6986 PD4103a NCBI-37 12 24474406 + 12 67632790 + 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 17 2 25657305/IL26_5048:4:109:15799:17022 PD4103a NCBI-37 12 29269685 - 12 30278440 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 19 5 4 25668655 PD4103a NCBI-37 12 57159655 - 12 77940008 + 0 0 Ensembl58 intron1 intergenic HSD17B6 ENSG00000025423 ENST00000322165 1 8630 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 11 8 25670650/IL26_5048:4:85:10097:11403 PD4103a NCBI-37 12 64286995 - 12 69565157 + 4 AAAT 0 Ensembl58 intron1 intergenic SRGAP1 ENSG00000196935 ENST00000355086 1 57522 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 95 21 8 IL26_5048:3:105:4870:12623 PD4103a NCBI-37 12 66754780 - 12 71950360 - 1 T 0 Ensembl58 intron22 intron5 GRIP1 LGR5 ENSG00000155974 ENSG00000139292 ENST00000398016 ENST00000266674 -1 1 23426 8549 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 22 4 25672371 PD4103a NCBI-37 12 66768955 + 12 67096036 - 0 3 CTG Ensembl58 intron21 intergenic GRIP1 ENSG00000155974 ENST00000398016 -1 23426 amplicon_associated somatic BWA-0.5.8 BRASS-0 4 2 IL26_5048:1:38:10165:5475 PD4103a NCBI-37 12 67087718 + 12 67105019 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 8 2 IL26_5048:1:40:6510:13177 PD4103a NCBI-37 12 67114138 + 12 109245345 + 1 A 0 Ensembl58 intergenic intron2 SSH1 ENSG00000084112 ENST00000326495 -1 54434 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 2 IL26_5048:1:111:17512:19329 PD4103a NCBI-37 12 67877403 - 12 73560059 + 0 99 GTTCAAATTTTGGTTATGTGTTTTATATAGTGTCACTATAGCCATCATAACAAGATTTCACAGAAGGCTGTCTCAAAAAACCAAAAAATTAAACAGATG Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 8 IL26_5048:1:105:1774:11865 PD4103a NCBI-37 12 67907314 + 12 68726830 + 0 0 Ensembl58 intergenic intron1 ENSG00000251695 ENSG00000251695 ENST00000504589 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 2 IL26_5048:4:11:14134:11530 PD4103a NCBI-37 12 68117852 + 12 68149661 + 1 A 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL26_5048:3:40:4895:9927 PD4103a NCBI-37 12 70079540 - 12 70590865 + 5 TTTAA 0 Ensembl58 intron4 intergenic BEST3 ENSG00000127325 ENST00000361403 -1 144453 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 26 8 IL26_5048:4:61:16282:13819 PD4103a NCBI-37 12 70974105 - 12 71023459 + 2 AA 0 Ensembl58 intron10 intron2 PTPRB PTPRB ENSG00000127329 ENSG00000127329 ENST00000334414 ENST00000334414 -1 -1 5787 5787 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 12 8 IL26_5048:2:31:2539:6423 PD4103a NCBI-37 12 71005870 + 12 72508223 + 1 A 0 Ensembl58 intron3 intergenic PTPRB ENSG00000127329 ENST00000334414 -1 5787 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 23 2 IL26_5048:4:73:15687:17202 PD4103a NCBI-37 12 71006332 + 12 77966322 + 2 AC 0 Ensembl58 intron3 intergenic PTPRB ENSG00000127329 ENST00000334414 -1 5787 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 14 1 25687874 PD4103a NCBI-37 12 72505363 + 12 73445648 - 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 5 1 IL26_5048:4:6:8618:1776 PD4103a NCBI-37 12 72550058 + 12 72553119 - 2 TC 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 9 1 IL26_5048:1:109:10774:17780 PD4103a NCBI-37 12 73482167 + 12 77966156 + 0 7 AGTTCCC Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 8 2 IL26_5048:1:66:11602:17490 PD4103a NCBI-37 12 73515627 - 12 73531390 + 6 CCAAAG 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 31 8 25698379 PD4103a NCBI-37 12 110429220 + 19 41659030 + 0 0 Ensembl58 intron2 intergenic GIT2 ENSG00000139436 ENST00000320063 -1 9815 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL26_5048:3:8:9301:17791 PD4103a NCBI-37 12 67984530 + 19 48661777 + 0 20 AAGAAAGCAGGAAGCATATG Ensembl58 intergenic intron4 LIG1 ENSG00000105486 ENST00000263274 -1 3978 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:1:119:12919:5400 PD4103a NCBI-37 12 28082804 + 20 39169670 + 2 TT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25657052 PD4103a NCBI-37 12 28123875 - 20 46305065 - 1 A 0 Ensembl58 intron1 intron10 PTHLH SULF2 ENSG00000087494 ENSG00000196562 ENST00000395872 ENST00000361612 -1 -1 5744 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 IL26_5048:4:27:14948:2894 PD4103a NCBI-37 16 73678343 + 16 73691500 - 2 TG 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL26_5048:2:88:12400:5932 PD4103a NCBI-37 16 57712505 - X 45356034 - 0 0 Ensembl58 intron4 intergenic GPR97 ENSG00000182885 ENST00000333493 1 222487 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25809092/IL26_5048:4:5:2506:12495 PD4103a NCBI-37 17 7497895 + 17 7935678 + 1 C 0 Ensembl58 intron9 intergenic FXR2 ENSG00000129245 ENST00000250113 -1 9513 deletion somatic MAQ-0.7.1 capillary_sequencing 23 4 2 IL26_5048:1:113:15434:15439 PD4103a NCBI-37 2 132994841 + 2 178469024 + 4 TAAA 0 Ensembl58 intron1 intron1 C21orf99 ENSG00000237655 ENSG00000163046 ENSG00000237655 ENST00000470729 ENST00000357045 -1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 25024380 PD4103a NCBI-37 2 142270191 + 2 142646932 + 3 CAT 0 Ensembl58 intron2 intron1 LRP1B LRP1B ENSG00000168702 ENSG00000168702 ENST00000389484 ENST00000389484 -1 -1 53353 53353 deletion somatic BWA-0.5.8 BRASS-0 11 2 25040459 PD4103a NCBI-37 2 191011353 - 20 20694214 + 1 T 0 Ensembl58 intron1 intergenic C2orf88 ENSG00000187699 ENST00000396974 1 84281 interchromosomal somatic BWA-0.5.8 BRASS-0 23 32 IL26_5048:1:98:6901:16683 PD4103a NCBI-37 2 234361403 - 5 9834538 - 0 2 CT Ensembl58 intron18 intron4 DGKD ENSG00000249781 ENSG00000077044 ENSG00000249781 ENST00000264057 ENST00000511616 1 -1 8527 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25036052 PD4103a NCBI-37 2 179793908 + 8 36943273 - 0 15 CATAGTATTCCAGAA Ensembl58 intron7 intergenic CCDC141 ENSG00000163492 ENST00000420890 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 25844873 PD4103a NCBI-37 20 16387999 - 20 19967295 + 0 0 Ensembl58 intron15 intron4 KIF16B RIN2 ENSG00000089177 ENSG00000132669 ENST00000354981 ENST00000440354 -1 1 55614 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 21 8 25847235 PD4103a NCBI-37 20 31478235 + 20 38457357 + 1 T 0 Ensembl58 intron7 intergenic EFCAB8 ENSG00000215529 ENST00000440534 1 388795 deletion somatic BWA-0.5.8 BRASS-0 22 2 25849056/IL26_5048:1:87:8725:13424 PD4103a NCBI-37 20 41309062 + 20 45322469 + 0 0 Ensembl58 intron6 intergenic PTPRT ENSG00000196090 ENST00000373187 -1 11122 deletion somatic MAQ-0.7.1 capillary_sequencing 23 3 2 IL26_5048:4:14:10336:13777 PD4103a NCBI-37 20 52412671 + 20 52538556 - 2 TC 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 25850925 PD4103a NCBI-37 20 52137509 - 21 37576725 + 0 0 Ensembl58 intergenic intron4 DOPEY2 ENSG00000142197 ENST00000399151 1 9980 interchromosomal somatic BWA-0.5.8 BRASS-0 20 32 IL26_5048:1:31:6822:14640 PD4103a NCBI-37 20 53050417 + 21 40471884 + 1 A 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25851893 PD4103a NCBI-37 20 55610458 - 21 40396057 - 0 1 T Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 25852002 PD4103a NCBI-37 20 56300314 + 21 42329640 - 0 1 G Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 IL26_5048:1:31:12704:8131 PD4103a NCBI-37 20 60980164 + 21 37554160 - 1 T 0 Ensembl58 intron1 intron2 CABLES2 DOPEY2 ENSG00000149679 ENSG00000142197 ENST00000279101 ENST00000399151 -1 1 81928 9980 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25852449/IL26_5048:2:92:1876:6773 PD4103a NCBI-37 20 61281682 + 21 27153575 + 1 C 0 Ensembl58 intron1 intron3 SLCO4A1 ENSG00000251052 ENSG00000101187 ENSG00000251052 ENST00000217159 ENST00000509807 1 1 28231 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 21 3 32 25855202/IL26_5048:4:48:5163:5733 PD4103a NCBI-37 21 36723622 - 21 39626774 + 0 0 Ensembl58 intron7 intergenic RUNX1 ENSG00000159216 ENST00000475045 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 88 11 8 IL26_5048:1:95:10758:15670 PD4103a NCBI-37 21 36986686 + 21 45946401 - 3 TGA 0 Ensembl58 intron5 intron7 RUNX1 C21orf29 ENSG00000159216 ENSG00000175894 ENST00000475045 ENST00000323084 -1 -1 54084 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 1 IL26_5048:4:42:12699:19152 PD4103a NCBI-37 21 37485283 + 21 39321648 + 2 GT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL26_5048:4:115:15078:1146 PD4103a NCBI-37 21 38083998 - 21 40506707 - 2 AT 0 Ensembl58 intron2 intergenic ENSG00000250811 ENSG00000250811 ENST00000430056 1 6493 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL26_5048:1:63:3132:1189 PD4103a NCBI-37 21 40741866 - 21 42469196 - 3 AGC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL26_5048:4:77:12224:16389 PD4103a NCBI-37 3 87318559 - 11 71846739 - 2 GA 0 Ensembl58 intron2 intergenic POU1F1 ENSG00000064835 ENST00000350375 -1 5449 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 27 32 IL26_5048:1:32:6067:14024 PD4103a NCBI-37 3 87891553 - 11 69187073 + 1 G 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 32 IL26_5048:4:20:5659:18869 PD4103a NCBI-37 3 73604356 - 12 73641172 - 2 AT 0 Ensembl58 intron3 intergenic PDZRN3 ENSG00000121440 ENST00000263666 -1 23024 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 45 32 IL26_5048:3:105:8166:17266 PD4103a NCBI-37 3 73679805 - 12 70954127 + 2 CC 0 Ensembl58 intergenic intron15 PTPRB ENSG00000127329 ENST00000261266 -1 5787 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:1:96:2215:3628 PD4103a NCBI-37 3 73742575 - 12 71406749 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 37 32 IL26_5048:4:61:9107:4365 PD4103a NCBI-37 3 73772946 + 12 73527016 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 36 32 IL26_5048:4:85:13668:1498 PD4103a NCBI-37 3 74033175 + 12 72779036 - 3 ATA 0 Ensembl58 intergenic intron3 TRHDE ENSG00000072657 ENST00000261180 1 29953 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 32 32 25082317 PD4103a NCBI-37 3 74035399 - 12 72560970 - 0 5 TAAAA Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 17 32 IL26_5048:4:13:3955:11179 PD4103a NCBI-37 3 74085534 - 12 72758993 + 2 TT 0 Ensembl58 intergenic intron2 TRHDE ENSG00000072657 ENST00000261180 1 29953 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 25 32 IL26_5048:2:17:13721:5645 PD4103a NCBI-37 3 74112799 + 12 68723594 + 0 0 Ensembl58 intergenic intron2 MDM1 ENSG00000111554 ENST00000430606 -1 56890 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:2:37:2611:15109 PD4103a NCBI-37 3 75185515 + 12 72790431 + 0 0 Ensembl58 intergenic intron3 TRHDE ENSG00000072657 ENST00000261180 1 29953 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 21 32 IL26_5048:1:20:14964:6582 PD4103a NCBI-37 3 77589256 - 12 70985036 + 1 T 0 Ensembl58 intron6 intron7 ROBO2 PTPRB ENSG00000185008 ENSG00000127329 ENST00000461745 ENST00000334414 1 -1 6092 5787 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 24 32 IL26_5048:2:51:14590:8952 PD4103a NCBI-37 3 77589707 + 12 71005789 + 1 T 0 Ensembl58 intron6 intron3 ROBO2 PTPRB ENSG00000185008 ENSG00000127329 ENST00000461745 ENST00000334414 1 -1 6092 5787 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 38 32 25085423 PD4103a NCBI-37 3 77837019 + 12 73437460 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 283 32 IL26_5048:1:13:17398:15706 PD4103a NCBI-37 3 78268479 + 12 73514347 - 3 TAA 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 13 32 IL26_5048:4:52:11910:6506 PD4103a NCBI-37 3 78273044 - 12 71058973 - 1 T 0 Ensembl58 intergenic intron6 PTPRR ENSG00000153233 ENST00000440835 -1 5801 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL26_5048:4:108:14881:19446 PD4103a NCBI-37 3 78320874 - 12 73483984 + 0 0 Ensembl58 intron1 intergenic ENSG00000240241 ENSG00000240241 ENST00000496674 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 10 32 25088934 PD4103a NCBI-37 3 87415349 + 12 72015289 - 1 C 0 Ensembl58 intergenic intron24 ZFC3H1 ENSG00000133858 ENST00000378743 -1 196441 amplicon_associated somatic BWA-0.5.8 BRASS-0 18 32 IL26_5048:1:113:7961:7927 PD4103a NCBI-37 3 87767046 + 12 72203197 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 26 32 IL26_5048:2:17:3549:3508 PD4103a NCBI-37 3 88520063 - 12 65049397 - 0 1 A Ensembl58 intergenic intron1 RASSF3 ENSG00000153179 ENST00000336061 1 283349 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25082130/IL26_5048:4:111:16601:3149 PD4103a NCBI-37 3 73674893 + 3 78348961 - 1 G 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 237 37 1 IL26_5048:2:69:18213:5480 PD4103a NCBI-37 3 73677620 - 3 78255551 + 0 3 GCT Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 10 8 IL26_5048:3:59:14856:14358 PD4103a NCBI-37 3 73678965 + 3 78285021 - 3 TGG 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 17 1 IL26_5048:3:75:4897:6829 PD4103a NCBI-37 3 74032861 - 3 74162953 - 0 29 ATCAGTGATTTCACGATGCTGCCATCTCT Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 34 4 IL26_5048:3:85:10177:18348 PD4103a NCBI-37 3 74037451 - 3 78303040 - 3 CTG 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 48 4 IL26_5048:1:59:15531:16992 PD4103a NCBI-37 3 74094192 + 3 74161765 + 2 TG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 25 2 25082483/IL26_5048:3:118:12495:5488 PD4103a NCBI-37 3 74140615 + 3 77543098 - 3 AAG 0 Ensembl58 intergenic intron5 ROBO2 ENSG00000185008 ENST00000461745 1 6092 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 293 31 1 IL26_5048:3:40:4499:15918 PD4103a NCBI-37 3 75182814 - 3 78335751 - 2 TT 0 Ensembl58 intergenic intron2 ENSG00000240241 ENSG00000240241 ENST00000496674 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 14 4 IL26_5048:4:97:12375:3017 PD4103a NCBI-37 3 77520038 - 3 77835702 + 0 0 Ensembl58 intron2 intergenic ROBO2 ENSG00000185008 ENST00000461745 1 6092 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 56 8 25089971 PD4103a NCBI-37 3 87902048 + 3 88182628 + 0 13 GGGATCTTTTCTA Ensembl58 intergenic intron2 CGGBP1 ENSG00000163320 ENST00000462901 -1 8545 amplicon_associated somatic BWA-0.5.8 BRASS-0 11 2 25078084/IL26_5048:2:84:9916:11156 PD4103a NCBI-37 3 64615310 + 4 144428794 + 0 2 CA Ensembl58 intron16 intergenic ADAMTS9 ENSG00000163638 ENST00000498707 -1 56999 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 13 3 32 IL26_5048:1:49:14739:20815 PD4103a NCBI-37 3 88186990 + 8 110968885 - 0 55 AAACAGCCTGCCCAGGTCACACAGAAAGTCAGGAGGAAGAACCGGAACTATGGTT Ensembl58 intron2 intergenic CGGBP1 ENSG00000163320 ENST00000462901 -1 8545 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:1:20:10201:1743 PD4103a NCBI-37 4 123882191 + 10 25085051 + 0 0 Ensembl58 intron9 intergenic SPATA5 ENSG00000145375 ENST00000274008 1 166378 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 9 32 25201465/IL26_5048:2:33:18837:8721 PD4103a NCBI-37 4 124863190 + 10 28081487 - 2 AG 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 37 7 32 IL26_5048:4:66:14450:8739 PD4103a NCBI-37 4 125066642 - 10 21954494 + 0 0 Ensembl58 intergenic intron8 MLLT10 ENSG00000078403 ENST00000377059 1 8028 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:1:89:15931:2472 PD4103a NCBI-37 4 125223112 + 10 7750374 + 2 AT 0 Ensembl58 intergenic intron3 ITIH2 ENSG00000151655 ENST00000358415 1 3698 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:2:62:4296:16287 PD4103a NCBI-37 4 126109093 - 10 28020970 + 2 TA 0 Ensembl58 intergenic intron5 MKX ENSG00000150051 ENST00000419761 -1 283078 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL26_5048:1:2:11391:20321 PD4103a NCBI-37 4 126111144 + 10 22206195 - 8 ATAATTTA 0 Ensembl58 intergenic intron6 DNAJC1 ENSG00000136770 ENST00000376980 -1 64215 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 32 IL26_5048:4:40:5988:20627 PD4103a NCBI-37 4 128352581 - 10 28082891 - 0 2 AC Ensembl58 intron1 intergenic ENSG00000248491 ENSG00000248491 ENST00000504050 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:2:89:14914:14188 PD4103a NCBI-37 4 128479223 - 10 20088863 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:4:45:8027:19335 PD4103a NCBI-37 4 129178788 - 10 7669132 + 3 TTA 0 Ensembl58 intergenic intron5 ITIH5 ENSG00000123243 ENST00000256861 -1 80760 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:1:110:11931:19875 PD4103a NCBI-37 4 146028501 - 10 25405995 - 1 C 0 Ensembl58 intron3 intron2 ABCE1 ENSG00000231422 ENSG00000164163 ENSG00000231422 ENST00000455563 ENST00000436140 1 1 6059 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:2:82:3439:6733 PD4103a NCBI-37 4 147596573 + 10 19845071 - 0 0 Ensembl58 intergenic intron4 C10orf112 ENSG00000204740 ENST00000377265 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 32 IL26_5048:2:62:7506:6658 PD4103a NCBI-37 4 154806468 + 10 24726803 - 2 AA 0 Ensembl58 intergenic intron3 KIAA1217 ENSG00000120549 ENST00000430453 1 56243 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:4:48:12913:10229 PD4103a NCBI-37 4 154980740 + 10 21952239 - 0 3 GGA Ensembl58 intergenic intron8 MLLT10 ENSG00000078403 ENST00000377059 1 8028 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 IL26_5048:3:21:17018:7044 PD4103a NCBI-37 4 87171246 - 10 21778325 + 0 0 Ensembl58 intron2 intergenic MAPK10 ENSG00000109339 ENST00000513186 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:1:27:7178:16568 PD4103a NCBI-37 4 76718195 - 19 53343400 + 2 CT 0 Ensembl58 intron12 intron3 USO1 ZNF28 ENSG00000138768 ENSG00000198538 ENST00000508939 ENST00000438150 1 -1 7576 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25201009 PD4103a NCBI-37 4 123648910 - 4 126478950 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 22 8 IL26_5048:2:29:3919:1906 PD4103a NCBI-37 4 124514903 - 4 146042755 + 0 0 Ensembl58 intergenic intron13 ABCE1 ENSG00000164163 ENST00000455563 1 6059 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 8 IL26_5048:3:114:14139:17245 PD4103a NCBI-37 4 124544629 + 4 129254968 - 1 A 0 Ensembl58 intergenic intron3 ENSG00000251432 ENSG00000251432 ENST00000509834 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 1 25201272 PD4103a NCBI-37 4 124552615 - 4 145740536 + 3 TCT 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 38 8 IL26_5048:2:120:19263:14177 PD4103a NCBI-37 4 125149862 - 4 125976927 - 1 A 0 Ensembl58 intron1 intergenic ENSG00000249837 ENSG00000249837 ENST00000507299 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 4 IL26_5048:1:75:17753:11480 PD4103a NCBI-37 4 125198533 + 4 125875437 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 2 IL26_5048:4:30:8194:20295 PD4103a NCBI-37 4 125955411 + 4 154761548 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 2 IL26_5048:4:39:11574:8233 PD4103a NCBI-37 4 126027515 + 4 128439486 - 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 1 25201893/IL26_5048:3:98:11686:7998 PD4103a NCBI-37 4 126206461 + 4 143788888 - 2 GG 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 12 3 1 IL26_5048:2:97:7829:19281 PD4103a NCBI-37 4 126531494 + 4 126741661 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 7 2 IL26_5048:3:56:15566:10828 PD4103a NCBI-37 4 128371996 + 4 129280898 - 1 A 0 Ensembl58 intron1 intron3 ENSG00000248491 ENSG00000251432 ENSG00000248491 ENSG00000251432 ENST00000504050 ENST00000509834 -1 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 9 1 IL26_5048:4:34:2973:9273 PD4103a NCBI-37 4 129240170 + 4 154696292 + 1 T 0 Ensembl58 intron3 intergenic ENSG00000251432 ENSG00000251432 ENST00000509834 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 2 IL26_5048:4:117:9202:10597 PD4103a NCBI-37 4 131643653 + 4 149387205 + 0 68 CATTCATCAGCTTGAGGACTAAAATAGTGACTTGCAATTTTCATGTAGTAGGTACTTAGTACTTACTA Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 2 25208297 PD4103a NCBI-37 4 143780393 - 4 163564694 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 7 4 25213160/IL26_5048:2:111:17606:2626 PD4103a NCBI-37 4 150427652 + 4 153678729 + 1 T 0 Ensembl58 intron14 intergenic ENSG00000234828 ENSG00000234828 ENST00000425891 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 41 7 2 IL26_5048:4:26:3153:14924 PD4103a NCBI-37 4 154999468 - 4 155005812 - 1 T 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 25219652 PD4103a NCBI-37 4 166555941 - 4 169354749 + 0 0 Ensembl58 intergenic intron10 DDX60L ENSG00000181381 ENST00000260184 -1 91351 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 8 8 25174064 PD4103a NCBI-37 4 60937546 - 4 67874067 - 2 TT 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 15 4 25180969 PD4103a NCBI-37 4 74484230 - 4 76990647 - 0 14 AGCATATTTTATGG Ensembl58 intron1 intron1 RASSF6 ART3 ENSG00000169435 ENSG00000156219 ENST00000307439 ENST00000341029 -1 1 166824 419 amplicon_associated somatic BWA-0.5.8 BRASS-0 13 4 IL26_5048:1:80:18121:15605 PD4103a NCBI-37 4 74690749 + 4 89053158 - 0 10 TTATTATGGA Ensembl58 intergenic intron3 ABCG2 ENSG00000118777 ENST00000237612 -1 9429 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 1 IL26_5048:1:3:13108:18699 PD4103a NCBI-37 4 87239658 + 4 124979093 + 1 T 0 Ensembl58 intron2 intergenic MAPK10 ENSG00000109339 ENST00000513186 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 2 25186535 PD4103a NCBI-37 4 87531497 - 4 125960254 + 1 T 0 Ensembl58 intron1 intergenic PTPN13 ENSG00000163629 ENST00000411767 1 5783 amplicon_associated somatic BWA-0.5.8 BRASS-0 21 8 IL26_5048:4:118:11049:3567 PD4103a NCBI-37 4 88912432 - 4 88918827 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL26_5048:2:14:11867:8293 PD4103a NCBI-37 4 164858893 + X 30230369 - 2 CC 0 Ensembl58 intron2 intergenic Mar-01 ENSG00000145416 ENST00000507270 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:3:22:19408:11272 PD4103a NCBI-37 5 153763540 - 12 71462294 + 2 TG 0 Ensembl58 intron6 intergenic GALNT10 ENSG00000164574 ENST00000297107 1 55568 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL26_5048:2:88:10562:14305 PD4103a NCBI-37 5 60357630 + 12 68648078 - 4 AGAT 0 Ensembl58 intron1 intergenic NDUFAF2 ENSG00000164182 ENST00000296597 1 91942 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 25255588 PD4103a NCBI-37 5 37264159 - 20 31481442 + 0 0 Ensembl58 intergenic intron9 EFCAB8 ENSG00000215529 ENST00000440534 1 388795 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 25249992/IL26_5048:2:47:16247:11006 PD4103a NCBI-37 5 23872664 + 5 32149706 + 0 13 GATGTTACCTGAC Ensembl58 intergenic intron1 GOLPH3 ENSG00000113384 ENST00000265070 -1 64083 deletion somatic MAQ-0.7.1 capillary_sequencing 22 3 2 25258858 PD4103a NCBI-37 5 38337410 + 5 54138289 - 2 CT 0 Ensembl58 intron1 intron4 EGFLAM ENSG00000232517 ENSG00000164318 ENSG00000232517 ENST00000339580 ENST00000426589 1 -1 133584 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 13 1 IL26_5048:4:65:5589:7022 PD4103a NCBI-37 5 54485287 - 5 54488199 + 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 25244578 PD4103a NCBI-37 5 18242991 + 7 86140009 - 0 29 CTCGTTTTCAAAATCCCCACAGCACATTT Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 15 32 25254522/IL26_5048:1:12:19328:20392 PD4103a NCBI-37 5 32393344 + 8 41675884 + 5 TTAAA 0 Ensembl58 intron11 intron1 ZFR ANK1 ENSG00000056097 ENSG00000029534 ENST00000265069 ENST00000265709 -1 -1 51663 286 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 24 6 32 25336149 PD4103a NCBI-37 6 100411128 - 6 163838906 - 1 T 0 Ensembl58 intron1 intron1 MCHR2 QKI ENSG00000152034 ENSG00000112531 ENST00000281806 ENST00000361758 -1 1 84539 9444 tandem_duplication somatic BWA-0.5.8 BRASS-0 8 4 25395866 PD4103a NCBI-37 7 119424439 + 7 134670400 - 0 0 Ensembl58 intron2 intergenic ENSG00000225546 ENSG00000225546 ENST00000426413 -1 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 22 1 25386162 PD4103a NCBI-37 7 69920055 + 7 70156502 + 1 C 0 Ensembl58 intron5 intron5 AUTS2 AUTS2 ENSG00000158321 ENSG00000158321 ENST00000342771 ENST00000342771 1 1 26053 26053 deletion somatic BWA-0.5.8 BRASS-0 5 2 25386244 PD4103a NCBI-37 7 70171697 + 7 70238891 + 2 TT 0 Ensembl58 intron6 intron11 AUTS2 AUTS2 ENSG00000158321 ENSG00000158321 ENST00000342771 ENST00000342771 1 1 26053 26053 deletion somatic BWA-0.5.8 BRASS-0 7 2 25387399 PD4103a NCBI-37 7 75587774 + 7 124439759 + 1 C 0 Ensembl58 intron2 intergenic POR ENSG00000127948 ENST00000265302 1 5447 deletion somatic BWA-0.5.8 BRASS-0 4 2 25388610 PD4103a NCBI-37 7 82861998 - 7 131691211 - 1 A 0 Ensembl58 intergenic intron1 ENSG00000236238 ENSG00000236238 ENST00000457638 1 tandem_duplication somatic BWA-0.5.8 BRASS-0 19 4 25390387 PD4103a NCBI-37 7 88534807 - 7 134543806 + 0 90 CCAGCTACTCAGGAAGCTGAGGCAGGAGAATCACTTGGACCCAGGAGGCAGAGGTTGCAGTGAGCCAAGATTGTGCCACTGAACTCCAGC Ensembl58 intron1 intron2 ZNF804B CALD1 ENSG00000182348 ENSG00000122786 ENST00000333190 ENST00000361388 1 1 219578 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 6 8 25395055 PD4103a NCBI-37 7 117221667 - 8 31049081 + 1 A 0 Ensembl58 intron11 intergenic CFTR ENSG00000001626 ENST00000003084 1 1080 interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 IL26_5048:2:68:9078:9664 PD4103a NCBI-37 8 125009420 - 10 56805500 + 2 AA 0 Ensembl58 intron11 intron3 FER1L6 PCDH15 ENSG00000214814 ENSG00000150275 ENST00000399018 ENST00000373957 1 -1 654463 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 27 32 IL26_5048:3:102:4021:7151 PD4103a NCBI-37 8 132782637 - 10 55331312 - 3 TTG 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 25486003 PD4103a NCBI-37 8 126096937 - 11 80034083 + 3 CTG 0 Ensembl58 intron1 intergenic KIAA0196 ENSG00000164961 ENST00000318410 -1 9897 amplicon_associated somatic BWA-0.5.8 BRASS-0 16 32 IL26_5048:4:105:17206:7200 PD4103a NCBI-37 8 127299890 - 11 67714482 - 1 G 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 10 32 IL26_5048:4:10:3140:2798 PD4103a NCBI-37 8 129209057 - 11 68947623 + 3 AAG 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 32 IL26_5048:4:46:8778:20999 PD4103a NCBI-37 8 130343990 - 11 71836534 + 0 2 TC Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 48 32 IL26_5048:2:71:12207:8065 PD4103a NCBI-37 8 130363451 + 11 73831409 - 0 0 Ensembl58 intergenic intron8 C2CD3 ENSG00000168014 ENST00000313663 -1 26005 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 39 32 IL26_5048:4:79:6230:10334 PD4103a NCBI-37 8 42259941 - 11 80658969 - 0 1 T Ensembl58 intron8 intergenic VDAC3 ENSG00000078668 ENST00000417062 1 7419 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 25423582 PD4103a NCBI-37 8 43079562 - 11 73683094 + 8 TGGCAGGC 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 228 32 IL26_5048:2:99:19687:6372 PD4103a NCBI-37 8 85004010 - 11 69064248 - 2 TG 0 Ensembl58 intergenic 3UTR MYEOV ENSG00000172927 ENST00000308946 1 26579 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 25456304/IL26_5048:1:95:10156:5471 PD4103a NCBI-37 8 91185028 + 11 76806487 - 0 1 T Ensembl58 intergenic intron3 CAPN5 ENSG00000149260 ENST00000278559 1 726 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 97 18 32 25484455/IL26_5048:1:71:15679:14663 PD4103a NCBI-37 8 125014414 - 12 69551142 + 0 0 Ensembl58 intron11 intergenic FER1L6 ENSG00000214814 ENST00000399018 1 654463 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 124 27 32 IL26_5048:4:100:12309:2782 PD4103a NCBI-37 8 127134592 + 12 73578595 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:2:10:3649:3828 PD4103a NCBI-37 8 127299630 + 12 70590655 - 2 TT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 12 32 IL26_5048:1:11:15128:4224 PD4103a NCBI-37 8 128016133 - 12 67963349 + 3 CAT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25488514 PD4103a NCBI-37 8 129554030 + 12 84724671 - 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 7 32 25488877/IL26_5048:3:62:3292:2230 PD4103a NCBI-37 8 130017282 + 12 84758865 + 0 36 GAGTTTTAATAGGCTCACAGTTCTGCATGGCTGGGA Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 11 5 32 IL26_5048:3:87:12092:12253 PD4103a NCBI-37 8 131789455 + 12 25699957 + 1 C 0 Ensembl58 intergenic intron3 IFLTD1 ENSG00000152936 ENST00000413632 -1 160492 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:1:7:13826:8455 PD4103a NCBI-37 8 132230541 - 12 70593534 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 25456048/IL26_5048:3:74:7073:13529 PD4103a NCBI-37 8 90985098 - 12 66857149 - 1 T 0 Ensembl58 intron5 intron8 NBN GRIP1 ENSG00000104320 ENSG00000155974 ENST00000265433 ENST00000398016 -1 -1 4683 23426 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 15 3 32 IL26_5048:4:85:10287:20941 PD4103a NCBI-37 8 38799288 + 20 29920274 + 0 0 Ensembl58 intron3 intergenic PLEKHA2 ENSG00000169499 ENST00000388745 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL26_5048:1:13:17452:10595 PD4103a NCBI-37 8 110878006 - 8 125592441 - 0 59 AGGATATGAGACTATCTTACCAAGCACCTAGTGGACAAAGAAGATGCCATCCTCAGCGG Ensembl58 intergenic intron6 MTSS1 ENSG00000170873 ENST00000325064 -1 9788 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 13 4 25476246 PD4103a NCBI-37 8 112225870 + 8 122829108 - 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 6 1 IL26_5048:3:7:18364:13863 PD4103a NCBI-37 8 125011289 + 8 125012607 - 1 A 0 Ensembl58 intron11 intron11 FER1L6 FER1L6 ENSG00000214814 ENSG00000214814 ENST00000399018 ENST00000399018 1 1 654463 654463 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 25 1 IL26_5048:2:90:18810:7610 PD4103a NCBI-37 8 125876498 + 8 129423651 - 0 0 Ensembl58 intron1 intergenic ENSG00000235517 ENSG00000235517 ENST00000422573 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 10 1 IL26_5048:4:81:13332:7930 PD4103a NCBI-37 8 125942362 + 8 128740960 - 0 0 Ensembl58 intergenic intron1 ENSG00000249375 ENSG00000249375 ENST00000502463 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 9 1 IL26_5048:4:100:14455:1266 PD4103a NCBI-37 8 126642700 - 8 128862241 + 3 TGT 0 Ensembl58 intergenic intron1 PVT1 ENSG00000249859 ENST00000504719 1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 10 8 IL26_5048:1:37:16665:11296 PD4103a NCBI-37 8 127296730 - 8 127308303 - 2 GG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 IL26_5048:3:33:17238:15671 PD4103a NCBI-37 8 129291395 + 8 130218879 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 2 25421871 PD4103a NCBI-37 8 34971784 + 8 36009016 + 1 A 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 21 2 IL26_5048:4:75:13788:2647 PD4103a NCBI-37 8 35546577 - 8 111013217 - 2 AT 0 Ensembl58 intron7 intergenic UNC5D ENSG00000156687 ENST00000404895 1 137970 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 IL26_5048:3:94:12422:11784 PD4103a NCBI-37 8 36106238 + 8 36110881 + 2 TA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 IL26_5048:1:39:17083:17109 PD4103a NCBI-37 8 86933265 + 8 98357956 - 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 14 1 25455947/IL26_5048:2:90:15930:7238 PD4103a NCBI-37 8 90772304 - 8 132480740 - 1 G 0 Ensembl58 intron1 intergenic RIPK2 ENSG00000104312 ENST00000220751 1 8767 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 33 3 4 IL26_5048:4:47:15334:12697 PD4103a NCBI-37 8 91704587 + 8 125774304 + 0 0 Ensembl58 intergenic intron1 ENSG00000235517 ENSG00000235517 ENST00000422573 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 14 2 25464506/IL26_5048:3:9:10788:8160 PD4103a NCBI-37 8 98297839 - 8 125846269 - 4 CCTA 0 Ensembl58 intergenic intron1 ENSG00000235517 ENSG00000235517 ENST00000422573 -1 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 78 13 4 IL26_5048:4:3:5137:1191 PD4103a NCBI-37 9 9274105 + 9 9534986 + 2 TG 0 Ensembl58 intron8 intron7 PTPRD PTPRD ENSG00000153707 ENSG00000153707 ENST00000381196 ENST00000381196 -1 -1 5789 5789 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 25499293 PD4103a NCBI-37 9 9329040 + 9 9518978 + 2 TT 0 Ensembl58 intron8 intron7 PTPRD PTPRD ENSG00000153707 ENSG00000153707 ENST00000381196 ENST00000381196 -1 -1 5789 5789 deletion somatic BWA-0.5.8 BRASS-0 8 2 25499354 PD4103a NCBI-37 9 9647188 + 9 10276021 + 0 2 CT Ensembl58 intron6 intron2 PTPRD PTPRD ENSG00000153707 ENSG00000153707 ENST00000381196 ENST00000381196 -1 -1 5789 5789 deletion somatic BWA-0.5.8 BRASS-0 5 2 25863942 PD4103a NCBI-37 X 72212182 - X 87535081 + 1 T 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 3 8 IL29_5178:2:78:18124:14943 PD4107a NCBI-37 1 163606884 - 1 163608453 - 2 AA 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:1:68:9976:6346 PD4107a NCBI-37 1 205783268 - 1 208221787 - 1 G 0 Ensembl58 intergenic intron17 PLXNA2 ENSG00000076356 ENST00000367033 -1 5362 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 27134650 PD4107a NCBI-37 1 209201548 - 1 210197016 - 4 ATCT 0 Ensembl58 intergenic intron4 SYT14 ENSG00000143469 ENST00000472886 1 255928 tandem_duplication somatic BWA-0.5.8 BRASS-0 5 4 IL29_5178:2:13:5921:12035 PD4107a NCBI-37 1 210173090 + 1 210177901 - 2 CT 0 Ensembl58 intron2 intron2 SYT14 SYT14 ENSG00000143469 ENSG00000143469 ENST00000472886 ENST00000472886 1 1 255928 255928 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL29_5178:4:25:7545:1837 PD4107a NCBI-37 1 214009743 - 1 214015150 - 1 G 0 Ensembl58 intron3 intron3 ENSG00000230461 ENSG00000230461 ENSG00000230461 ENSG00000230461 ENST00000433082 ENST00000433082 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:4:40:17998:13490 PD4107a NCBI-37 1 223383893 - 1 223390661 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27070033 PD4107a NCBI-37 1 51314154 + 1 87003567 + 1 G 0 Ensembl58 intron2 intergenic FAF1 ENSG00000185104 ENST00000396153 -1 11124 deletion somatic BWA-0.5.8 BRASS-0 7 2 IL29_5178:4:19:8854:8219 PD4107a NCBI-37 1 32144921 + 14 73658033 - 1 T 0 Ensembl58 intron42 intron6 COL16A1 PSEN1 ENSG00000084636 ENSG00000080815 ENST00000373672 ENST00000324501 -1 1 1307 5663 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 27094148 PD4107a NCBI-37 1 96803775 + 2 43872589 - 0 0 Ensembl58 intron3 intron2 ENSG00000231987 PLEKHH2 ENSG00000231987 ENSG00000152527 ENST00000435311 ENST00000282406 -1 1 130271 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 IL29_5178:4:5:5801:17965 PD4107a NCBI-37 1 72639225 - 6 128519292 + 1 A 0 Ensembl58 intron1 intron6 NEGR1 PTPRK ENSG00000172260 ENSG00000152894 ENST00000357731 ENST00000368226 -1 -1 257194 5796 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL29_5178:1:84:15599:6971 PD4107a NCBI-37 10 115410741 - 10 115415212 - 0 0 Ensembl58 intron7 intron4 NRAP NRAP ENSG00000197893 ENSG00000197893 ENST00000359988 ENST00000359988 -1 -1 4892 4892 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27749848 PD4107a NCBI-37 10 122686152 - 10 124184314 - 0 0 Ensembl58 intron1 intron8 ENSG00000227307 PLEKHA1 ENSG00000227307 ENSG00000107679 ENST00000414774 ENST00000433307 -1 1 59338 tandem_duplication somatic BWA-0.5.8 BRASS-0 7 4 IL29_5178:3:32:9870:9205 PD4107a NCBI-37 10 26610763 - 10 26626848 - 4 AGAC 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 27731743/IL29_5178:2:89:13821:18942 PD4107a NCBI-37 10 65195648 + 12 56106092 + 1 G 0 Ensembl58 intron1 intergenic JMJD1C ENSG00000171988 ENST00000399262 -1 221037 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 12 3 32 IL29_5178:2:70:4076:14570 PD4107a NCBI-37 10 62027848 - 14 94962342 - 2 GA 0 Ensembl58 intron5 intron4 ANK3 SERPINA12 ENSG00000151150 ENSG00000165953 ENST00000280772 ENST00000341228 -1 -1 288 145264 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL29_5178:2:92:7515:17592 PD4107a NCBI-37 11 127565431 + 11 131668625 - 0 0 Ensembl58 intergenic intron1 OPCML ENSG00000182667 ENST00000374791 1 50863 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 7 1 IL29_5178:1:17:15084:9657 PD4107a NCBI-37 11 95890098 - 11 95946626 + 1 T 0 Ensembl58 intron1 intron1 MAML2 MAML2 ENSG00000184384 ENSG00000184384 ENST00000440572 ENST00000440572 -1 -1 84441 84441 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27777607 PD4107a NCBI-37 11 69844811 + 16 75237494 + 1 T 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 9 32 IL29_5178:1:40:10206:11657 PD4107a NCBI-37 12 102256829 - 12 102282234 - 0 0 Ensembl58 intergenic intron1 DRAM1 ENSG00000136048 ENST00000258534 1 55332 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:2:54:16362:11618 PD4107a NCBI-37 12 102558507 + 12 102561574 + 2 AT 0 Ensembl58 intron3 intron4 C12orf48 C12orf48 ENSG00000185480 ENSG00000185480 ENST00000457614 ENST00000457614 1 1 55010 55010 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:1:61:18024:16260 PD4107a NCBI-37 12 10504961 - 12 10768734 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:4:24:7510:16773 PD4107a NCBI-37 12 2633301 - 12 6204602 - 0 0 Ensembl58 intron9 intron6 CACNA1C VWF ENSG00000151067 ENSG00000110799 ENST00000347598 ENST00000261405 1 -1 775 7450 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27810147/IL29_5178:1:27:12590:2937 PD4107a NCBI-37 12 41496475 + 12 61562808 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 20 4 2 27814332 PD4107a NCBI-37 12 62365896 + 12 66286229 + 0 6 CTGCAC Ensembl58 intron1 intron3 FAM19A2 HMGA2 ENSG00000198673 ENSG00000149948 ENST00000393663 ENST00000403681 -1 1 338811 8091 deletion somatic BWA-0.5.8 BRASS-0 12 2 IL29_5178:2:70:1234:8205 PD4107a NCBI-37 16 17667492 - 16 17672143 - 2 TG 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL29_5178:2:114:19225:6878 PD4107a NCBI-37 16 31447009 - 16 31451951 - 4 AGTT 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 IL29_5178:1:50:13968:10598 PD4107a NCBI-37 16 56460752 - 16 56468157 - 4 TTCA 0 Ensembl58 intergenic intron6 NUDT21 ENSG00000167005 ENST00000300291 -1 11051 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 8 4 IL29_5178:1:34:17481:1227 PD4107a NCBI-37 16 87425115 + 16 87426698 + 3 CTG 0 Ensembl58 intergenic intron1 MAP1LC3B ENSG00000140941 ENST00000268607 1 81631 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL29_5178:3:71:18578:5291 PD4107a NCBI-37 19 12630403 - 19 12642810 - 0 0 Ensembl58 intron1 intron1 ENSG00000196826 ZNF564 ENSG00000196826 ENSG00000249709 ENST00000428311 ENST00000339282 -1 -1 163051 163050 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27200003 PD4107a NCBI-37 2 115208150 - 19 52697863 + 1 A 0 Ensembl58 intron1 intron1 DPP10 PPP2R1A ENSG00000175497 ENSG00000105568 ENST00000410059 ENST00000322088 1 1 57628 5518 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 IL29_5178:4:17:14211:17826 PD4107a NCBI-37 2 179509450 - 2 179513087 - 2 GC 0 Ensembl58 intron166 intron165 TTN TTN ENSG00000155657 ENSG00000155657 ENST00000356127 ENST00000356127 -1 -1 7273 7273 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27166684 PD4107a NCBI-37 2 31207853 - 2 201339517 + 0 5 TTCCG Ensembl58 intron2 intron12 GALNT14 SPATS2L ENSG00000158089 ENSG00000196141 ENST00000349752 ENST00000409988 -1 1 79623 26010 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 7 8 27186396/IL29_5178:3:26:18006:1733 PD4107a NCBI-37 2 68233849 + 2 222689712 - 0 10 CAGAAACTTC Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 14 3 1 27245691 PD4107a NCBI-37 2 232253938 + 9 16774965 - 1 A 0 Ensembl58 intron1 intron1 ENSG00000224376 BNC2 ENSG00000224376 ENSG00000173068 ENST00000415129 ENST00000380672 1 -1 54796 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 IL29_5178:1:92:15985:8743 PD4107a NCBI-37 22 23546693 - 22 23567654 - 2 TG 0 Ensembl58 intron1 intron1 BCR BCR ENSG00000186716 ENSG00000186716 ENST00000359540 ENST00000359540 1 1 613 613 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27959370 PD4107a NCBI-37 22 29758976 - 22 30698763 - 6 GAGTAG 0 Ensembl58 intron3 intron2 AP1B1 TBC1D10A ENSG00000100280 ENSG00000099992 ENST00000356015 ENST00000215790 -1 -1 83874 tandem_duplication somatic BWA-0.5.8 BRASS-0 11 4 27959392 PD4107a NCBI-37 22 29815139 - 22 30698769 - 0 3 CAG Ensembl58 intron2 intron2 AP1B1 TBC1D10A ENSG00000100280 ENSG00000099992 ENST00000415447 ENST00000215790 -1 -1 162 83874 tandem_duplication somatic BWA-0.5.8 BRASS-0 7 4 IL29_5178:3:100:7727:6672 PD4107a NCBI-37 3 148913662 - 3 148921377 - 0 0 Ensembl58 intron9 intron6 CP CP ENSG00000047457 ENSG00000047457 ENST00000264613 ENST00000264613 -1 -1 1356 1356 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL29_5178:1:112:15572:1927 PD4107a NCBI-37 3 159955647 - 3 159958166 - 1 A 0 Ensembl58 intron18 intron18 ENSG00000248710 ENSG00000248710 ENSG00000248710 ENSG00000248710 ENST00000483754 ENST00000483754 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL29_5178:4:31:16819:19616 PD4107a NCBI-37 3 165748041 + 3 165751405 + 3 TAC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 27277937 PD4107a NCBI-37 3 71396733 - 3 72378725 - 2 GC 0 Ensembl58 intron4 intergenic FOXP1 ENSG00000114861 ENST00000318779 -1 27086 tandem_duplication somatic BWA-0.5.8 BRASS-0 4 4 IL29_5178:2:72:7417:10501 PD4107a NCBI-37 4 164652389 + 16 31948946 - 8 CAGAAATC 0 Ensembl58 intron3 intergenic Mar-01 ENSG00000145416 ENST00000507270 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL29_5178:4:24:16669:10061 PD4107a NCBI-37 4 130382843 + 4 130386909 + 3 TAG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL29_5178:1:39:15912:20441 PD4107a NCBI-37 4 56512678 - 4 56522692 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 27390865 PD4107a NCBI-37 4 141099800 + 6 168568214 + 3 TCA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 18 32 IL29_5178:1:81:11656:11387 PD4107a NCBI-37 5 65251073 + 11 119537686 + 2 TC 0 Ensembl58 intron1 intron5 ERBB2IP PVRL1 ENSG00000112851 ENSG00000110400 ENST00000380943 ENST00000264025 1 -1 55914 5818 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 27447925 PD4107a NCBI-37 5 163199484 + 15 81790439 + 2 TA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 IL29_5178:2:9:19563:9055 PD4107a NCBI-37 5 31422695 + 5 31514450 + 0 0 Ensembl58 intron26 intron5 RNASEN RNASEN ENSG00000113360 ENSG00000113360 ENST00000344624 ENST00000344624 -1 -1 29102 29102 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 27422193/IL29_5178:1:90:10079:20837 PD4107a NCBI-37 5 55448215 + 5 119510134 + 0 0 Ensembl58 intron6 intergenic ANKRD55 ENSG00000164512 ENST00000341048 -1 79722 deletion somatic MAQ-0.7.1 capillary_sequencing 18 3 2 IL29_5178:2:44:8918:6927 PD4107a NCBI-37 5 85881882 + 5 154163001 + 0 0 Ensembl58 intergenic intron1 LARP1 ENSG00000155506 ENST00000377643 1 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:1:60:13118:2410 PD4107a NCBI-37 6 131140895 - 16 87065621 + 1 C 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 27492679 PD4107a NCBI-37 6 112797149 + 6 112885633 + 0 5 TGTGT Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 8 2 IL29_5178:2:48:2631:2472 PD4107a NCBI-37 6 121466870 + 6 121467528 + 0 0 Ensembl58 intron24 intron24 C6orf170 C6orf170 ENSG00000146350 ENSG00000146350 ENST00000368464 ENST00000368464 -1 -1 221322 221322 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 27495920 PD4107a NCBI-37 6 123092970 - 6 154466402 + 1 A 0 Ensembl58 intergenic intron3 OPRM1 ENSG00000112038 ENST00000337049 1 4988 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 16 8 27496602 PD4107a NCBI-37 6 124809960 - 6 138229745 - 0 1 T Ensembl58 intron3 intergenic NKAIN2 ENSG00000188580 ENST00000368417 1 154215 amplicon_associated somatic BWA-0.5.8 BRASS-0 33 4 IL29_5178:2:58:17164:10176 PD4107a NCBI-37 6 125699216 - 6 130440529 - 0 0 Ensembl58 intergenic intron19 L3MBTL3 ENSG00000198945 ENST00000368136 1 84456 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:3:41:5018:21191 PD4107a NCBI-37 6 126430736 - 6 134019485 + 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL29_5178:4:62:18169:12057 PD4107a NCBI-37 6 127644164 - 6 133941629 + 0 0 Ensembl58 intron4 intergenic ECHDC1 ENSG00000093144 ENST00000368289 -1 55862 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 IL29_5178:4:39:10085:15701 PD4107a NCBI-37 6 127757361 + 6 137286143 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 IL29_5178:3:27:4585:11805 PD4107a NCBI-37 6 130293330 + 6 134022568 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 IL29_5178:2:6:5616:13608 PD4107a NCBI-37 6 130293549 - 6 133882797 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:3:27:15263:1674 PD4107a NCBI-37 6 130809360 - 6 132552676 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:4:69:18319:15382 PD4107a NCBI-37 6 131470069 + 6 133411833 + 0 0 Ensembl58 intron1 intron2 AKAP7 ENSG00000231023 ENSG00000118507 ENSG00000231023 ENST00000368123 ENST00000457339 1 1 9465 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:4:23:12022:17582 PD4107a NCBI-37 6 131578497 + 6 133990175 - 0 0 Ensembl58 intron2 intergenic AKAP7 ENSG00000118507 ENST00000263050 1 9465 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL29_5178:1:100:19099:1676 PD4107a NCBI-37 6 131677395 + 6 131787092 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:1:47:19246:3175 PD4107a NCBI-37 6 132447355 + 6 133482349 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL29_5178:4:115:16235:4455 PD4107a NCBI-37 6 132602717 + 6 138076788 + 3 AAG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:1:108:13089:7260 PD4107a NCBI-37 6 134554292 - 6 137276434 - 2 TT 0 Ensembl58 intron2 intergenic SGK1 ENSG00000118515 ENST00000367858 -1 6446 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL29_5178:3:21:10672:7267 PD4107a NCBI-37 6 134624890 - 6 137988887 + 0 0 Ensembl58 intron1 intergenic SGK1 ENSG00000118515 ENST00000367858 -1 6446 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 8 8 27505614 PD4107a NCBI-37 6 135316402 - 6 139777056 - 3 GGT 0 Ensembl58 intron6 intergenic HBS1L ENSG00000112339 ENST00000415177 -1 10767 amplicon_associated somatic BWA-0.5.8 BRASS-0 9 4 27486903 PD4107a NCBI-37 6 88607990 + 6 90946570 - 2 TG 0 Ensembl58 intergenic intron1 BACH2 ENSG00000112182 ENST00000343122 -1 60468 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 13 1 27492673 PD4107a NCBI-37 6 112796862 - X 45156316 + 3 TGG 0 Ensembl58 intergenic intron2 ENSG00000229491 ENSG00000229491 ENST00000438181 1 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 27520777 PD4107a NCBI-37 7 4820813 + 18 6964195 + 0 1 T Ensembl58 exon2 intron51 KIAA0415 LAMA1 ENSG00000242802 ENSG00000101680 ENST00000348624 ENST00000389658 1 -1 9907 284217 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 IL29_5178:1:78:19666:7367 PD4107a NCBI-37 7 120137431 - 7 120141772 - 2 TA 0 Ensembl58 intron1 intron1 KCND2 KCND2 ENSG00000184408 ENSG00000184408 ENST00000331113 ENST00000331113 1 1 3751 3751 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 IL29_5178:4:105:17024:20090 PD4107a NCBI-37 7 123337345 + 7 123379937 + 0 0 Ensembl58 intron5 intron1 WASL WASL ENSG00000106299 ENSG00000106299 ENST00000223023 ENST00000223023 -1 -1 8976 8976 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL29_5178:2:103:17766:14806 PD4107a NCBI-37 7 70182162 + 7 70213632 + 2 AG 0 Ensembl58 intron6 intron6 AUTS2 AUTS2 ENSG00000158321 ENSG00000158321 ENST00000342771 ENST00000342771 1 1 26053 26053 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL29_5178:1:51:6595:18010 PD4107a NCBI-37 7 91532092 - 7 91543349 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 27580946/IL29_5178:2:115:1788:3250 PD4107a NCBI-37 7 95558684 - 7 96178484 - 2 GG 0 Ensembl58 intron6 intron2 DYNC1I1 SHFM1 ENSG00000158560 ENSG00000127922 ENST00000324972 ENST00000466986 1 -1 1780 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 15 4 4 27555048 PD4107a NCBI-37 7 46609605 + 9 98522389 - 0 52 TATATTATATTATATTATATTATATTATATATATATATTATATTATATTATA Ensembl58 intergenic intron2 C9orf130 ENSG00000175611 ENST00000433656 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 27656313 PD4107a NCBI-37 8 116567107 - 16 89408666 + 2 GG 0 Ensembl58 intron5 intron2 TRPS1 ANKRD11 ENSG00000104447 ENSG00000167522 ENST00000395715 ENST00000301030 -1 -1 7227 29123 interchromosomal somatic BWA-0.5.8 BRASS-0 9 32 27633099 PD4107a NCBI-37 8 52094670 + 17 80908561 - 1 T 0 Ensembl58 intergenic intron11 B3GNTL1 ENSG00000175711 ENST00000320865 -1 146712 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 IL29_5178:4:70:1801:3113 PD4107a NCBI-37 9 12359550 - 9 12363755 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL29_5178:1:67:13310:17067 PD4107a NCBI-37 9 34338965 + 9 34340963 + 3 CCA 0 Ensembl58 intron3 intron4 NUDT2 NUDT2 ENSG00000164978 ENSG00000164978 ENST00000337747 ENST00000337747 1 1 318 318 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL29_5178:2:113:4796:14970 PD4107a NCBI-37 X 110461316 - X 110463344 - 2 TG 0 Ensembl58 intron18 intron18 PAK3 PAK3 ENSG00000077264 ENSG00000077264 ENST00000372010 ENST00000372010 1 1 5063 5063 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 IL29_5178:3:51:16954:2004 PD4107a NCBI-37 X 73056898 + X 73063844 + 0 0 Ensembl58 intron2 XIST XIST ENSG00000229807 ENSG00000229807 ENST00000429829 ENST00000429829 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL29_5178:1:85:5081:12268 PD4107a NCBI-37 X 98369980 + X 98371017 + 2 TC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL16_5041:2:26:12573:3153 PD4109a NCBI-37 1 113235955 - 1 113307734 - 0 95 AACTCACTTCCTGCAGTAATCTTTCCTTGAACAAACTCACCCTCTAATTCCCACCTGCAATTGTGTGTAGAAATCCATTACGTGTGTAATTTTTG Ensembl58 intron6 intergenic MOV10 ENSG00000155363 ENST00000357443 1 4343 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL16_5041:2:42:13004:12335 PD4109a NCBI-37 1 154056305 + 1 154354291 + 0 0 Ensembl58 intron16 intergenic NUP210L ENSG00000143552 ENST00000368559 -1 91181 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 27129145 PD4109a NCBI-37 1 155021053 - 1 155300249 - 6 CACGCC 0 Ensembl58 intron16 exon10 DCST1 RUSC1 ENSG00000163357 ENSG00000160753 ENST00000295542 ENST00000368352 1 1 149095 23623 tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 IL16_5041:2:78:11333:14691 PD4109a NCBI-37 1 188015962 - 1 188058649 - 1 A 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 14 4 IL16_5041:3:34:9850:11122 PD4109a NCBI-37 1 188038597 - 1 188041319 + 0 4 GACA Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 IL16_5041:2:97:3239:9138 PD4109a NCBI-37 1 109781333 + 8 41525064 + 2 TG 0 Ensembl58 intergenic intron40 ANK1 ENSG00000029534 ENST00000265709 -1 286 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL16_5041:3:99:12625:16671 PD4109a NCBI-37 10 54870432 + 10 54878935 + 4 TTCT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 27897903 PD4109a NCBI-37 10 78341277 + 10 82644191 - 1 G 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 3 1 27886827 PD4109a NCBI-37 10 37199786 - 12 39954463 - 0 1 G Ensembl58 intergenic intron9 ABCD2 ENSG00000173208 ENST00000308666 -1 225 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 IL16_5041:3:102:13916:3605 PD4109a NCBI-37 10 73967237 - 17 75824974 + 0 0 Ensembl58 intron3 intergenic ASCC1 ENSG00000138303 ENST00000317126 -1 51008 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 27882185 PD4109a NCBI-37 10 22275186 + X 70283385 + 4 ATTT 0 Ensembl58 intron1 intron1 DNAJC1 SNX12 ENSG00000136770 ENSG00000147164 ENST00000376980 ENST00000374274 -1 -1 64215 29934 interchromosomal somatic BWA-0.5.8 BRASS-0 11 32 27875188 PD4109a NCBI-37 10 6222611 - X 127551159 - 2 CT 0 Ensembl58 intron1 intron2 PFKFB3 ENSG00000225689 ENSG00000170525 ENSG00000225689 ENST00000379789 ENST00000449485 1 -1 5209 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 27901793 PD4109a NCBI-37 10 95153337 + X 29625437 + 0 4 CATC Ensembl58 intron16 intron5 MYOF IL1RAPL1 ENSG00000138119 ENSG00000169306 ENST00000359263 ENST00000378993 -1 1 26509 11141 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 27913129 PD4109a NCBI-37 11 20841950 + 11 21507067 + 0 1 T Ensembl58 intron3 intron15 NELL1 NELL1 ENSG00000165973 ENSG00000165973 ENST00000357134 ENST00000357134 1 1 4745 4745 deletion somatic BWA-0.5.8 BRASS-0 7 2 IL16_5041:2:89:7725:6444 PD4109a NCBI-37 11 43081181 - 11 43091624 - 0 6 CCATCT Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL16_5041:4:58:3447:20676 PD4109a NCBI-37 12 110344630 - 12 110370301 - 4 TATC 0 Ensembl58 intron5 3UTR TCHP GIT2 ENSG00000139437 ENSG00000139436 ENST00000312777 ENST00000355312 1 -1 84260 9815 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 28016941 PD4109a NCBI-37 16 77938840 - 16 78243574 - 1 C 0 Ensembl58 intron7 intron5 VAT1L WWOX ENSG00000171724 ENSG00000186153 ENST00000302536 ENST00000408984 1 1 57687 51741 tandem_duplication somatic BWA-0.5.8 BRASS-0 11 4 28017029 PD4109a NCBI-37 16 78804352 + 16 79014678 + 3 GGG 0 Ensembl58 intron8 intron8 WWOX WWOX ENSG00000186153 ENSG00000186153 ENST00000408984 ENST00000408984 1 1 51741 51741 deletion somatic BWA-0.5.8 BRASS-0 9 2 28034659/IL16_5041:4:88:8515:8417 PD4109a NCBI-37 19 2648209 + 19 6096924 + 3 AGA 0 Ensembl58 intron1 intron1 GNG7 RFX2 ENSG00000176533 ENSG00000087903 ENST00000382159 ENST00000303657 -1 -1 2788 5990 deletion somatic MAQ-0.7.1 capillary_sequencing 18 8 2 28037565 PD4109a NCBI-37 19 32094394 - 19 47094573 + 0 17 TCTAATGAATGTTATGA Ensembl58 intron2 intron1 ENSG00000232700 ENSG00000230510 ENSG00000232700 ENSG00000230510 ENST00000441786 ENST00000414155 1 -1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 17 8 28034738/IL16_5041:2:43:15464:8544 PD4109a NCBI-37 19 3569010 + 19 17382934 - 0 18 TATCACTAACATACCTAA Ensembl58 intron4 intron3 RAX2 C19orf62 ENSG00000173976 ENSG00000105393 ENST00000328906 ENST00000359435 -1 1 84839 29086 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 18 4 1 IL16_5041:3:15:10635:11161 PD4109a NCBI-37 2 198796367 + 13 105453588 + 0 1 A Ensembl58 intron1 intergenic PLCL1 ENSG00000115896 ENST00000487695 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL16_5041:1:89:7782:19096 PD4109a NCBI-37 2 219036366 + 13 105493621 + 4 TCTG 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL16_5041:4:40:11094:3412 PD4109a NCBI-37 2 153262439 + 2 153329805 + 2 CA 0 Ensembl58 intron1 intron1 FMNL2 FMNL2 ENSG00000157827 ENSG00000157827 ENST00000288670 ENST00000288670 1 1 114793 114793 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL16_5041:1:24:3828:4393 PD4109a NCBI-37 4 125316411 - 19 10650438 + 0 11 AGTTTAAATTT Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL16_5041:1:107:5946:3600 PD4109a NCBI-37 4 102260347 + 4 102262796 + 1 A 0 Ensembl58 intron1 intron1 PPP3CA PPP3CA ENSG00000138814 ENSG00000138814 ENST00000507176 ENST00000507176 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL16_5041:4:102:12444:14958 PD4109a NCBI-37 4 74792822 - 4 74889795 + 0 10 CCTCTTCACN Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 27531914 PD4109a NCBI-37 5 6718569 - 12 19523604 - 2 GA 0 Ensembl58 intron1 intron26 PAPD7 PLEKHA5 ENSG00000112941 ENSG00000052126 ENST00000230859 ENST00000424268 1 1 11044 54477 interchromosomal somatic BWA-0.5.8 BRASS-0 5 32 27678721/IL16_5041:4:61:11195:2549 PD4109a NCBI-37 6 157627134 + 11 28744140 + 1 A 0 Ensembl58 intergenic intron1 ENSG00000249867 ENSG00000249867 ENST00000513853 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 10 3 32 27678008/IL16_5041:4:90:15511:8056 PD4109a NCBI-37 6 154716093 + 13 106631210 + 1 A 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 3 32 IL16_5041:4:44:7036:2182 PD4109a NCBI-37 6 122875211 + 6 123109570 - 0 31 AGCATAAGGTTGTGGGGACATGTATATTTCT Ensembl58 intron2 intergenic PKIB ENSG00000135549 ENST00000392491 1 5570 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 IL16_5041:4:16:19162:6583 PD4109a NCBI-37 6 122909859 - 6 122911595 + 0 21 TTACATCTGATATATTTAGAG Ensembl58 intron3 intron3 PKIB PKIB ENSG00000135549 ENSG00000135549 ENST00000392491 ENST00000392491 1 1 5570 5570 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL16_5041:4:37:4222:2947 PD4109a NCBI-37 6 122922142 + 6 123110113 + 0 18 TGCTAAGAAAATCAGATG Ensembl58 intron3 intergenic PKIB ENSG00000135549 ENST00000392491 1 5570 deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 IL16_5041:1:51:5902:11590 PD4109a NCBI-37 6 123283656 + 6 123309764 - 0 5 TTATT Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 IL16_5041:2:62:19465:13591 PD4109a NCBI-37 6 15356820 + 6 15438523 + 3 TAA 0 Ensembl58 intron1 intron3 JARID2 JARID2 ENSG00000008083 ENSG00000008083 ENST00000341776 ENST00000341776 1 1 3720 3720 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL16_5041:2:29:17572:10650 PD4109a NCBI-37 6 27996590 - 6 28112287 + 0 6 TCAACT Ensembl58 intergenic intron1 ZNF192 ENSG00000198315 ENST00000330236 1 7745 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 6 4 IL16_5041:3:101:3373:3009 PD4109a NCBI-37 6 38193640 - 6 38273351 - 1 T 0 Ensembl58 intron8 intron6 BTBD9 BTBD9 ENSG00000183826 ENSG00000183826 ENST00000403056 ENST00000403056 -1 -1 114781 114781 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 27648878 PD4109a NCBI-37 6 96374977 - 6 101834412 + 2 TC 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 7 8 27650546/IL16_5041:2:114:14873:3788 PD4109a NCBI-37 6 99078296 + 8 117820049 - 4 GAAA 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 15 7 32 IL16_5041:4:71:14720:16411 PD4109a NCBI-37 7 153303454 - X 24569081 - 3 CCA 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL16_5041:4:50:12783:7238 PD4109a NCBI-37 8 55046077 + 8 122942922 - 3 GCT 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 7 1 27769638 PD4109a NCBI-37 8 59496488 - 8 87523159 - 0 0 Ensembl58 3UTR intron1 NSMAF CPNE3 ENSG00000035681 ENSG00000085719 ENST00000427130 ENST00000198765 -1 1 8439 8895 tandem_duplication somatic BWA-0.5.8 BRASS-0 18 4 27784444/IL16_5041:1:28:5512:13644 PD4109a NCBI-37 8 77066839 + 8 113587625 - 0 0 Ensembl58 intergenic intron23 CSMD3 ENSG00000164796 ENST00000395717 -1 114788 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 18 5 1 27787166 PD4109a NCBI-37 8 83570028 - 8 113587772 + 1 A 0 Ensembl58 intergenic intron23 CSMD3 ENSG00000164796 ENST00000395717 -1 114788 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 20 8 IL16_5041:4:26:6085:10893 PD4109a NCBI-37 X 128247086 + X 128250009 + 1 C 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL37_5081:4:19:14108:8794 PD4115a NCBI-37 1 165104365 + 1 184283103 + 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 8 1 24025506 PD4115a NCBI-37 1 154598954 - 11 39917812 + 1 A 0 Ensembl58 intron1 intergenic ADAR ENSG00000160710 ENST00000368471 -1 103 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 23980594 PD4115a NCBI-37 1 2816658 + 14 63908826 - 1 C 0 Ensembl58 intergenic intron3 PPP2R5E ENSG00000154001 ENST00000337537 -1 5529 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 IL37_5081:3:100:14250:19841 PD4115a NCBI-37 1 87632222 - 17 61089990 - 1 T 0 Ensembl58 intron7 intron1 HS2ST1 TANC2 ENSG00000153936 ENSG00000170921 ENST00000370548 ENST00000424789 1 1 26115 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 IL37_5081:3:32:13939:15065 PD4115a NCBI-37 1 87632227 + 17 61089271 + 3 CAG 0 Ensembl58 intron7 intron1 HS2ST1 TANC2 ENSG00000153936 ENSG00000170921 ENST00000370548 ENST00000424789 1 1 26115 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 IL37_5081:4:23:18536:19010 PD4115a NCBI-37 10 61519864 - 10 126103603 + 4 CCAC 0 Ensembl58 intergenic intron1 OAT ENSG00000065154 ENST00000368845 -1 4942 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 24539065 PD4115a NCBI-37 10 30507404 + 18 10198601 + 2 AG 0 Ensembl58 intron1 intergenic ENSG00000250659 ENSG00000250659 ENST00000502624 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 22 32 24540227/IL37_5081:3:43:7835:18888 PD4115a NCBI-37 10 36685757 - 19 23214750 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 7 4 32 IL37_5081:1:58:6366:4242 PD4115a NCBI-37 11 92417371 + 11 92417890 + 2 TG 0 Ensembl58 intron2 intron2 FAT3 FAT3 ENSG00000165323 ENSG00000165323 ENST00000409404 ENST00000409404 1 1 120114 120114 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:1:14:7002:6861 PD4115a NCBI-37 12 51169989 + 12 68416775 + 4 TCAG 0 Ensembl58 intron1 intergenic ATF1 ENSG00000123268 ENST00000262053 1 466 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 IL37_5081:2:7:13794:7751 PD4115a NCBI-37 13 26103995 + 13 87314170 + 2 GA 0 Ensembl58 intron2 intergenic ATP8A2 ENSG00000132932 ENST00000381655 1 51761 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:1:21:10356:4846 PD4115a NCBI-37 13 26107444 + 13 87314125 - 4 TGTG 0 Ensembl58 exon6 intergenic ATP8A2 ENSG00000132932 ENST00000381655 1 51761 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 24613324 PD4115a NCBI-37 13 27015106 - 13 54913034 + 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 15 8 24635680/IL37_5081:1:76:10289:8793 PD4115a NCBI-37 14 25548095 + 14 36210824 - 1 A 0 Ensembl58 intergenic intron11 RALGAPA1 ENSG00000174373 ENST00000389698 -1 253959 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 17 4 1 IL37_5081:3:75:11745:7771 PD4115a NCBI-37 17 71085803 + 17 71086734 + 1 G 0 Ensembl58 intron1 intron1 SLC39A11 SLC39A11 ENSG00000133195 ENSG00000133195 ENST00000255559 ENST00000255559 -1 -1 201266 201266 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL37_5081:3:72:4653:15794 PD4115a NCBI-37 17 77048528 + 17 77049760 + 1 C 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL37_5081:1:103:9939:11371 PD4115a NCBI-37 18 66004658 + 18 70682881 + 1 A 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 24086096 PD4115a NCBI-37 2 26004717 + 17 54706683 + 0 37 GGACGGGGTTTTGCCATATCGGCCAGGCTGTTCTTGA Ensembl58 intron3 intergenic ASXL2 ENSG00000143970 ENST00000497092 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 24104110/IL37_5081:1:105:8828:14785 PD4115a NCBI-37 2 65408460 + 17 15123225 + 1 T 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 12 3 32 IL37_5081:4:40:11294:14448 PD4115a NCBI-37 2 12155232 + 2 12155794 + 0 5 ACTAA Ensembl58 intron2 intron2 ENSG00000224184 ENSG00000224184 ENSG00000224184 ENSG00000224184 ENST00000412294 ENST00000412294 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 24132159/IL37_5081:3:18:17498:15768 PD4115a NCBI-37 2 135855670 + 2 180304688 + 0 63 GAGGCATCTGCAGTTACATTTTCCCCCTTGCTGGTCCTATGCAAAGTCAATATATCATTCCTT Ensembl58 intron5 intergenic RAB3GAP1 ENSG00000115839 ENST00000264158 1 22930 deletion somatic MAQ-0.7.1 capillary_sequencing 15 3 2 IL37_5081:3:94:14792:12213 PD4115a NCBI-37 2 151132161 + 2 151145492 + 3 GAA 0 Ensembl58 intron2 intron2 ENSG00000230645 ENSG00000230645 ENSG00000230645 ENSG00000230645 ENST00000437118 ENST00000437118 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:3:27:13784:1816 PD4115a NCBI-37 2 225250279 + 2 225255707 - 2 CC 0 Ensembl58 intron2 intron2 FAM124B FAM124B ENSG00000124019 ENSG00000124019 ENST00000389874 ENST00000389874 -1 -1 79843 79843 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 IL37_5081:4:118:12556:11088 PD4115a NCBI-37 2 239467335 - 2 239571841 + 3 TGG 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL37_5081:4:85:13215:16499 PD4115a NCBI-37 2 60651039 + 2 108981519 + 3 CTG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 IL37_5081:2:57:12094:8377 PD4115a NCBI-37 2 136993941 - 4 123427423 - 0 1 A Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL37_5081:4:93:13022:2683 PD4115a NCBI-37 2 136994551 + 4 123429457 + 2 TC 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL37_5081:2:84:14661:15543 PD4115a NCBI-37 2 66514062 - 6 23693922 + 6 TACAAA 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 24151633/IL37_5081:1:10:6673:9900 PD4115a NCBI-37 2 240353361 - 7 67827562 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 13 3 32 IL37_5081:2:113:16975:9600 PD4115a NCBI-37 20 10788441 - 20 10804250 + 2 GT 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL37_5081:2:24:19607:16986 PD4115a NCBI-37 22 42255801 + 22 42257372 + 0 0 Ensembl58 intron1 intron1 SREBF2 SREBF2 ENSG00000198911 ENSG00000198911 ENST00000361204 ENST00000361204 1 1 6721 6721 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 24198781 PD4115a NCBI-37 3 179804881 - 18 75118142 - 2 TG 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 14 32 24152846 PD4115a NCBI-37 3 1404739 + 3 153534255 + 0 1 A Ensembl58 intron12 intron3 CNTN6 ENSG00000240456 ENSG00000134115 ENSG00000240456 ENST00000350110 ENST00000488210 1 -1 27255 deletion somatic BWA-0.5.8 BRASS-0 17 2 24193513 PD4115a NCBI-37 3 153536117 + 3 179146776 - 4 TCTT 0 Ensembl58 intron3 intron1 ENSG00000240456 GNB4 ENSG00000240456 ENSG00000114450 ENST00000488210 ENST00000232564 -1 -1 59345 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 5 1 24195053 PD4115a NCBI-37 3 162146244 + 3 162328999 + 2 CA 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 17 2 24172101 PD4115a NCBI-37 3 71250680 + 3 79119256 + 2 TC 0 Ensembl58 intron5 intron3 FOXP1 ROBO1 ENSG00000114861 ENSG00000169855 ENST00000318789 ENST00000464233 -1 -1 27086 6091 deletion somatic BWA-0.5.8 BRASS-0 10 2 IL37_5081:1:119:1315:13343 PD4115a NCBI-37 4 131050072 + 4 131052123 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 24224537 PD4115a NCBI-37 4 60198233 - 4 129776693 - 0 0 Ensembl58 intergenic intron6 PHF17 ENSG00000077684 ENST00000413543 1 79960 tandem_duplication somatic BWA-0.5.8 BRASS-0 21 4 24227878/IL37_5081:4:26:10645:5645 PD4115a NCBI-37 4 66425314 + 4 105002941 + 4 ATAA 0 Ensembl58 intron3 intergenic EPHA5 ENSG00000145242 ENST00000354839 -1 2044 deletion somatic MAQ-0.7.1 capillary_sequencing 20 3 2 IL37_5081:1:66:13954:16918 PD4115a NCBI-37 4 107530524 - 6 157281573 - 0 65 AGTGTAGTTCCAGCTTCAGATAAGGAAAGGAAGTTTAGGGTGACAGGAAGAGAACACAGTAGCCA Ensembl58 intergenic intron4 ARID1B ENSG00000049618 ENST00000275248 1 57492 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 IL37_5081:3:20:2954:17774 PD4115a NCBI-37 5 133079406 - 5 167873605 - 0 8 GTGCTAGT Ensembl58 intergenic intron17 WWC1 ENSG00000113645 ENST00000265293 1 23286 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL37_5081:1:75:3037:14714 PD4115a NCBI-37 5 36498607 + 5 36499517 + 5 AAAAG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 24286342/IL37_5081:2:33:18329:4529 PD4115a NCBI-37 5 58193094 + 5 123196151 + 2 AC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 38 6 2 24284844 PD4115a NCBI-37 5 54257431 - 8 135317240 - 0 1 T Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 IL37_5081:2:10:2863:11294 PD4115a NCBI-37 6 25956840 + 15 89690409 - 3 AAT 0 Ensembl58 intergenic intron5 ABHD2 ENSG00000140526 ENST00000355100 1 11057 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 IL37_5081:1:111:13551:13651 PD4115a NCBI-37 6 23692740 + 6 23698499 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 24380403/IL37_5081:3:28:10428:6823 PD4115a NCBI-37 7 67826618 - 10 103908205 - 2 TG 0 Ensembl58 intergenic exon10 PPRC1 ENSG00000148840 ENST00000278070 1 23082 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 18 4 32 IL37_5081:3:15:15090:6247 PD4115a NCBI-37 7 124824674 + 7 124825521 + 2 CT 0 Ensembl58 intron2 intron2 ENSG00000237764 ENSG00000237764 ENSG00000237764 ENSG00000237764 ENST00000424515 ENST00000424515 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL37_5081:1:63:9601:4863 PD4115a NCBI-37 7 15168726 + 7 15170098 + 0 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:2:17:7863:5041 PD4115a NCBI-37 7 67071240 - 7 67073045 + 0 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL37_5081:3:117:18055:2833 PD4115a NCBI-37 7 83853384 + 7 137183429 - 3 TTG 0 Ensembl58 intron4 intron21 SEMA3A DGKI ENSG00000075213 ENSG00000157680 ENST00000489270 ENST00000288490 -1 -1 9162 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 IL37_5081:2:55:11290:13851 PD4115a NCBI-37 7 95588322 + 7 95598688 + 0 0 Ensembl58 intron6 intron6 DYNC1I1 DYNC1I1 ENSG00000158560 ENSG00000158560 ENST00000324972 ENST00000324972 1 1 1780 1780 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:1:16:12974:9266 PD4115a NCBI-37 8 102403605 + 12 13506435 + 1 A 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 2 32 IL37_5081:1:92:3398:3526 PD4115a NCBI-37 8 141958951 + 8 141967538 + 2 CA 0 Ensembl58 intron1 intron1 PTK2 PTK2 ENSG00000169398 ENSG00000169398 ENST00000340930 ENST00000340930 -1 -1 5747 5747 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 IL37_5081:1:40:10897:17911 PD4115a NCBI-37 8 24446911 + 8 24452260 + 1 T 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL37_5081:4:114:2244:8264 PD4115a NCBI-37 8 35758267 + 8 35759733 - 0 1 T Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 IL37_5081:1:5:14750:16429 PD4115a NCBI-37 8 36931419 - 8 53047435 - 2 AG 0 Ensembl58 intergenic intron19 ST18 ENSG00000147488 ENST00000276480 -1 9705 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 24424386 PD4115a NCBI-37 8 53301916 - 8 72896253 - 0 0 Ensembl58 intron2 intron3 ST18 ENSG00000235531 ENSG00000147488 ENSG00000235531 ENST00000276480 ENST00000457356 -1 1 9705 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 5 1 24428523 PD4115a NCBI-37 8 61587631 + 8 73691310 + 1 A 0 Ensembl58 intergenic intron1 KCNB2 ENSG00000182674 ENST00000329185 1 9312 deletion somatic BWA-0.5.8 BRASS-0 9 2 IL37_5081:4:76:8571:11315 PD4115a NCBI-37 8 65651734 - 8 73575861 - 0 0 Ensembl58 intron1 intron1 CYP7B1 KCNB2 ENSG00000172817 ENSG00000182674 ENST00000310193 ENST00000329185 -1 1 9420 9312 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 24432754 PD4115a NCBI-37 8 68328260 + 8 70502807 - 3 TCC 0 Ensembl58 intron1 intron8 ENSG00000245424 SULF1 ENSG00000245424 ENSG00000137573 ENST00000501209 ENST00000402687 1 1 23213 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 21 1 24435027/IL37_5081:3:77:15846:18676 PD4115a NCBI-37 8 72288281 - 8 73562950 + 3 TTT 0 Ensembl58 intergenic intron1 KCNB2 ENSG00000182674 ENST00000329185 1 9312 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 22 5 8 24506594 PD4115a NCBI-37 9 16842104 - 17 48658644 + 0 9 ATTATTTAA Ensembl58 intron1 intron9 BNC2 CACNA1G ENSG00000173068 ENSG00000006283 ENST00000380672 ENST00000354983 -1 1 54796 8913 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 IL37_5081:3:37:18964:5876 PD4115a NCBI-37 9 31451454 + 9 31453154 + 3 ACA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:8:27:19425:57532 PD4116a NCBI-37 1 209662208 + 1 209682437 + 1 T 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:6:27:4964:99802 PD4116a NCBI-37 1 217357524 - 1 229030056 + 2 TG 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 HS2_5434:6:65:8440:46987 PD4116a NCBI-37 1 217358035 - 1 229030344 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 7 4 HS2_5434:8:47:5292:81315 PD4116a NCBI-37 1 247049915 + 1 247287066 + 2 TA 0 Ensembl58 intron19 AHCTF1 ZNF124 ENSG00000153207 ENSG00000196418 ENST00000391829 ENST00000472531 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:7:4:20398:70648 PD4116a NCBI-37 1 116867487 + 2 31098883 + 5 TTCTT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:7:26:2043:165196 PD4116a NCBI-37 1 116867834 - 2 31098116 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 23973169 PD4116a NCBI-37 1 215992208 - 4 158874136 - 4 AAAA 0 Ensembl58 intron47 intergenic USH2A ENSG00000042781 ENST00000307340 -1 7399 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 23973386 PD4116a NCBI-37 1 217843170 + 4 77055595 - 0 32 AAAGATATTAAGATTAATATTAATATTAAGAA Ensembl58 intron4 intron4 SPATA17 NUP54 ENSG00000162814 ENSG00000138750 ENST00000366933 ENST00000264883 1 -1 128153 53371 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 23963535 PD4116a NCBI-37 1 144997720 + 6 46773204 - 0 0 Ensembl58 intron3 intron5 PDE4DIP MEP1A ENSG00000178104 ENSG00000112818 ENST00000369348 ENST00000230588 -1 1 653513 4224 interchromosomal somatic BWA-0.5.8 BRASS-0 8 32 23947232 PD4116a NCBI-37 1 22672041 + 7 121612621 - 2 AC 0 Ensembl58 intergenic exon4 PTPRZ1 ENSG00000106278 ENST00000393386 1 5803 interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 /HS2_5434:6:26:14242:10849523954740 PD4116a NCBI-37 1 112132769 - 8 95660232 + 0 1 G Ensembl58 intron1 intron4 RAP1A ESRP1 ENSG00000116473 ENSG00000104413 ENST00000356415 ENST00000423620 1 1 5906 54845 interchromosomal somatic BWA-0.5.8 BRASS-0 16 32 HS2_5434:6:3:18724:44328 PD4116a NCBI-37 1 119255853 + 8 75820327 - 0 0 Ensembl58 intergenic ENSG00000229911 ENSG00000229911 ENST00000427122 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:7:28:3687:12246/23955544 PD4116a NCBI-37 1 119256077 + 8 75820506 - 0 1 G Ensembl58 intergenic ENSG00000229911 ENSG00000229911 ENST00000427122 1 interchromosomal somatic BWA-0.5.8 BRASS-0 24 32 23971651 PD4116a NCBI-37 1 202435052 - 8 74185161 - 3 AAA 0 Ensembl58 intron1 intergenic PPP1R12B ENSG00000077157 ENST00000391959 1 4660 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 HS2_5434:7:27:4657:149737 PD4116a NCBI-37 10 116989102 + 10 117021322 - 0 0 Ensembl58 intron9 intron10 ATRNL1 ATRNL1 ENSG00000107518 ENSG00000107518 ENST00000355044 ENST00000355044 1 1 26033 26033 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 HS2_5434:7:7:13904:62973/24558139 PD4116a NCBI-37 10 49926329 - 20 30969636 + 2 TA 0 Ensembl58 intron1 intron4 WDFY4 ASXL1 ENSG00000128815 ENSG00000171456 ENST00000325239 ENST00000375687 1 1 57705 171023 interchromosomal somatic BWA-0.5.8 BRASS-0 17 32 HS2_5434:8:44:5567:105031 PD4116a NCBI-37 11 28416126 + 11 41852659 + 5 CCTTT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 HS2_5434:7:6:5575:68283/24581637 PD4116a NCBI-37 11 28816486 + 11 28931415 + 3 TGT 0 Ensembl58 intron2 intron2 ENSG00000249867 ENSG00000249867 ENSG00000249867 ENSG00000249867 ENST00000513853 ENST00000513853 1 1 deletion somatic BWA-0.5.8 BRASS-0 20 2 HS2_5434:8:47:2559:12597/24581680 PD4116a NCBI-37 11 28944464 + 11 32797406 - 0 30 CAGAAAAAAATATATATGGAAGAAGGGGGC Ensembl58 intron2 intron1 ENSG00000249867 CCDC73 ENSG00000249867 ENSG00000186714 ENST00000513853 ENST00000335185 1 -1 493860 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 17 1 HS2_5434:7:26:1581:193062 PD4116a NCBI-37 11 32796947 - 11 32811137 + 3 CAG 0 Ensembl58 intron1 intron1 CCDC73 CCDC73 ENSG00000186714 ENSG00000186714 ENST00000335185 ENST00000335185 -1 -1 493860 493860 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 HS2_5434:7:41:21065:70421 PD4116a NCBI-37 11 40389766 + 11 40423473 - 4 TTAG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 24591493 PD4116a NCBI-37 11 65014891 + 11 66219582 + 1 A 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 17 2 HS2_5434:7:47:13081:142749 PD4116a NCBI-37 11 67090824 + 11 68962913 + 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 2 HS2_5434:7:4:5603:47942/24592537 PD4116a NCBI-37 11 68314729 + 11 68977583 - 2 CC 0 Ensembl58 intron4 intergenic SAPS3 ENSG00000110075 ENST00000393799 1 55291 amplicon_associated somatic BWA-0.5.8 BRASS-0 23 1 24592679 PD4116a NCBI-37 11 68773764 - 11 76807599 - 1 C 0 Ensembl58 intron2 intron3 MRGPRF CAPN5 ENSG00000172935 ENSG00000149260 ENST00000309099 ENST00000278559 -1 1 116535 726 amplicon_associated somatic BWA-0.5.8 BRASS-0 52 4 HS2_5434:6:23:18814:136275 PD4116a NCBI-37 11 70007247 - 11 80060458 - 1 A 0 Ensembl58 intron16 intergenic ANO1 ENSG00000131620 ENST00000355303 1 55107 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 8 HS2_5434:8:8:16387:30389/24593789 PD4116a NCBI-37 11 71002802 + 11 76308309 + 1 T 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 129 2 HS2_5434:7:2:2951:87609 PD4116a NCBI-37 11 77230087 - 11 78726783 + 0 1 C Ensembl58 intergenic intron6 ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 16 8 HS2_5434:8:44:17226:89876/24595594 PD4116a NCBI-37 11 78518542 - 11 79982736 + 1 A 0 Ensembl58 intron14 intergenic ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic BWA-0.5.8 BRASS-0 48 8 HS2_5434:8:41:17591:113546 PD4116a NCBI-37 11 78776894 + 11 79140102 + 3 GGA 0 Ensembl58 intron5 intron1 ODZ4 ODZ4 ENSG00000149256 ENSG00000149256 ENST00000278550 ENST00000278550 -1 -1 26011 26011 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 9 2 24595747 PD4116a NCBI-37 11 78782857 - 11 79998742 - 2 TA 0 Ensembl58 intron4 intergenic ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic BWA-0.5.8 BRASS-0 53 4 HS2_5434:6:28:4496:22550 PD4116a NCBI-37 11 78952654 - 11 80036633 + 0 145 CCCACCTGGAACAGTTGTAGAGCAATCTGTGGTGGGGGCATGGTGCTAGTCTTTGGTAAAAAGCACCTAGGTGATTCTAATGCACCGCCAGGGTCAAGTAACTCTAAATCTAGTGCCTGACAGCAGCTCAGAGAAACAGGTGTAA Ensembl58 intron2 intergenic ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 8 HS2_5434:7:66:17883:92463 PD4116a NCBI-37 11 69198200 + 17 15113659 - 4 CAGT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:8:25:17643:100699 PD4116a NCBI-37 11 77224176 + 17 14808777 - 0 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 16 32 HS2_5434:6:48:9605:22783 PD4116a NCBI-37 11 77531534 + 17 14962362 - 2 AT 0 Ensembl58 intron1 intergenic RSF1 ENSG00000048649 ENST00000308488 -1 51773 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 24595556 PD4116a NCBI-37 11 78303592 + 17 18834745 - 1 C 0 Ensembl58 intergenic intergenic amplicon_associated somatic BWA-0.5.8 BRASS-0 110 32 24595585 PD4116a NCBI-37 11 78514073 - 17 20007584 - 3 GAA 0 Ensembl58 intron15 intron2 ODZ4 CYTSB ENSG00000149256 ENSG00000128487 ENST00000278550 ENST00000261503 -1 1 26011 92521 amplicon_associated somatic BWA-0.5.8 BRASS-0 34 32 HS2_5434:7:68:1894:25490/24595700 PD4116a NCBI-37 11 78726520 + 17 14159910 - 0 0 Ensembl58 intron6 intergenic ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic BWA-0.5.8 BRASS-0 46 32 HS2_5434:7:27:9843:108255 PD4116a NCBI-37 11 79068242 - 17 14350271 + 5 CTCTG 0 Ensembl58 intron1 intergenic ODZ4 ENSG00000149256 ENST00000278550 -1 26011 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 HS2_5434:8:6:10737:171119/24596092 PD4116a NCBI-37 11 80001484 - 17 15192049 + 1 C 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 55 32 24596114 PD4116a NCBI-37 11 80029310 + 17 14229522 + 3 ACT 0 Ensembl58 intergenic intron1 HS3ST3B1 ENSG00000125430 ENST00000360954 1 9953 amplicon_associated somatic BWA-0.5.8 BRASS-0 61 32 24596163 PD4116a NCBI-37 11 80079288 + 17 14105454 + 2 TT 0 Ensembl58 intergenic intron6 COX10 ENSG00000006695 ENST00000261643 1 1352 amplicon_associated somatic BWA-0.5.8 BRASS-0 112 32 HS2_5434:8:44:1380:77528 PD4116a NCBI-37 12 27121673 - 12 27128266 - 0 10 TAATGTGTGT Ensembl58 intergenic intron11 TM7SF3 ENSG00000064115 ENST00000343028 -1 51768 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 HS2_5434:7:68:20190:53618 PD4116a NCBI-37 12 54241995 + 13 45358757 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:6:7:8105:44847/24625229 PD4116a NCBI-37 12 95996974 + 15 41906585 + 0 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 19 32 HS2_5434:7:68:13489:76032 PD4116a NCBI-37 12 123362231 - X 92762350 + 3 TGA 0 Ensembl58 intron1 intergenic VPS37B ENSG00000139722 ENST00000267202 -1 79720 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:6:7:16880:35184 PD4116a NCBI-37 13 45918420 + 17 31517300 - 5 TTTCT 0 Ensembl58 intron2 intron1 ENSG00000170919 ACCN1 ENSG00000170919 ENSG00000108684 ENST00000405697 ENST00000359872 1 -1 40 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 HS2_5434:6:26:3035:45510 PD4116a NCBI-37 14 94667872 + 14 94676699 + 0 3 ACA Ensembl58 intron2 intron3 PPP4R4 PPP4R4 ENSG00000119698 ENSG00000119698 ENST00000304338 ENST00000304338 1 1 57718 57718 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 HS2_5434:7:48:19215:193170 PD4116a NCBI-37 17 14790363 + 17 15472419 - 1 G 0 Ensembl58 intron2 intron1 ENSG00000238212 CDRT1 ENSG00000238212 ENSG00000241322 ENST00000445035 ENST00000472534 1 -1 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 HS2_5434:6:2:19176:47456 PD4116a NCBI-37 17 17774836 - 17 18105987 - 50 AGTGATCCGCCTGCCTCAGCCTCCCGAAGTGCTGGAATTACAGGCGTGAG 0 Ensembl58 intron6 intron2 TOM1L2 ALKBH5 ENSG00000175662 ENSG00000091542 ENST00000318094 ENST00000399138 -1 1 146691 54890 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 HS2_5434:6:27:11740:25156 PD4116a NCBI-37 17 56449298 + 17 56459003 + 0 0 Ensembl58 intron2 intron2 RNF43 RNF43 ENSG00000108375 ENSG00000108375 ENST00000407977 ENST00000407977 -1 -1 54894 54894 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:7:48:14202:152149 PD4116a NCBI-37 17 59276939 + 17 59292008 + 1 G 0 Ensembl58 intron22 intron22 BCAS3 BCAS3 ENSG00000141376 ENSG00000141376 ENST00000390652 ENST00000390652 1 1 54828 54828 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 24722068 PD4116a NCBI-37 18 31739734 + 18 53139905 + 6 TTTTCT 0 Ensembl58 intron1 intron3 NOL4 TCF4 ENSG00000101746 ENSG00000196628 ENST00000261592 ENST00000356073 -1 -1 8715 6925 deletion somatic BWA-0.5.8 BRASS-0 15 2 HS2_5434:7:61:1720:186961 PD4116a NCBI-37 19 13465183 + 19 13571983 + 3 TGG 0 Ensembl58 intron6 intron1 CACNA1A CACNA1A ENSG00000141837 ENSG00000141837 ENST00000360228 ENST00000360228 -1 -1 773 773 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:6:45:4817:172298 PD4116a NCBI-37 2 102818026 + 2 227822372 + 0 0 Ensembl58 exon5 intron5 IL1RL2 RHBDD1 ENSG00000115598 ENSG00000144468 ENST00000264257 ENST00000392062 1 1 8808 84236 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:6:2:18753:80611 PD4116a NCBI-37 2 12411592 + 2 12416153 + 1 T 0 Ensembl58 intron3 intron3 ENSG00000224184 ENSG00000224184 ENSG00000224184 ENSG00000224184 ENST00000412294 ENST00000412294 1 1 deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 HS2_5434:6:66:7436:105256/23979398 PD4116a NCBI-37 2 16077672 - 2 195016067 + 2 TG 0 Ensembl58 intron3 intergenic MYCNOS ENSG00000233718 ENST00000420452 -1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 18 8 24086061 PD4116a NCBI-37 2 183701211 + 2 210014412 + 4 TTTA 0 Ensembl58 intron5 intergenic FRZB ENSG00000162998 ENST00000295113 -1 2487 deletion somatic BWA-0.5.8 BRASS-0 11 2 24090407 PD4116a NCBI-37 2 199378331 + 2 236646559 - 0 0 Ensembl58 intron3 intron3 PLCL1 AGAP1 ENSG00000115896 ENSG00000157985 ENST00000472193 ENST00000336665 1 1 116987 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 14 1 HS2_5434:8:3:20267:72574 PD4116a NCBI-37 2 202574001 - 2 204080754 + 2 GA 0 Ensembl58 intron27 intron54 ALS2 NBEAL1 ENSG00000003393 ENSG00000144426 ENST00000264276 ENST00000449802 -1 1 57679 65065 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 HS2_5434:8:64:12551:90661 PD4116a NCBI-37 2 204355866 + 2 227825727 - 2 CC 0 Ensembl58 intron3 intron5 RAPH1 RHBDD1 ENSG00000173166 ENSG00000144468 ENST00000319170 ENST00000392062 -1 1 65059 84236 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 24097976 PD4116a NCBI-37 2 226931250 - 2 242725917 + 0 9 GCTTTCTAC Ensembl58 intergenic intron1 GAL3ST2 ENSG00000154252 ENST00000192314 1 64090 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 18 8 HS2_5434:7:46:16190:189931 PD4116a NCBI-37 2 170528350 - 6 151013425 + 0 0 Ensembl58 intron4 intron2 C2orf77 PLEKHG1 ENSG00000154479 ENSG00000120278 ENST00000284676 ENST00000367328 -1 1 129881 57480 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 24097515 PD4116a NCBI-37 2 224980931 + 6 157226792 - 4 AGAA 0 Ensembl58 intergenic intron3 ARID1B ENSG00000049618 ENST00000275248 1 57492 interchromosomal somatic BWA-0.5.8 BRASS-0 8 32 HS2_5434:7:1:7585:67265 PD4116a NCBI-37 20 31578611 + 20 31605959 + 0 0 Ensembl58 intron8 intron7 SUN5 BPIL1 ENSG00000167098 ENSG00000078898 ENST00000356173 ENST00000170150 -1 1 140732 80341 deletion somatic MAQ-0.7.1 capillary_sequencing 12 2 HS2_5434:6:66:15736:154205 PD4116a NCBI-37 3 186201115 + 3 186205703 + 1 T 0 Ensembl58 intron2 intron2 ENSG00000224406 ENSG00000224406 ENSG00000224406 ENSG00000224406 ENST00000427914 ENST00000427914 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:6:48:21043:179956 PD4116a NCBI-37 3 186201785 + 3 188919772 + 2 CA 0 Ensembl58 intron2 intron1 ENSG00000224406 TPRG1 ENSG00000224406 ENSG00000188001 ENST00000427914 ENST00000345063 -1 1 285386 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:7:23:1505:136345 PD4116a NCBI-37 3 186202160 - 3 188919296 + 0 2 TC Ensembl58 intron2 intron1 ENSG00000224406 TPRG1 ENSG00000224406 ENSG00000188001 ENST00000427914 ENST00000345063 -1 1 285386 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 HS2_5434:7:65:5889:103568 PD4116a NCBI-37 3 186203251 - 3 186206389 - 0 79 CTTCATGGGGGTAGAGGTATCAGCATGAGAAAACACAGTTGACATCTTTGACTACACGCAGGCCACAGGGACTAACTTC Ensembl58 intron2 intron2 ENSG00000224406 ENSG00000224406 ENSG00000224406 ENSG00000224406 ENST00000427914 ENST00000427914 -1 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 HS2_5434:7:47:14063:116221 PD4116a NCBI-37 3 42849811 + 3 42856559 - 3 AAG 0 Ensembl58 intron1 intron1 ENSG00000235288 CCBP2 ENSG00000235288 ENSG00000144648 ENST00000449063 ENST00000422265 -1 1 1238 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 HS2_5434:7:8:7493:81546/24122557 PD4116a NCBI-37 3 44425922 + 3 53225877 + 2 GT 0 Ensembl58 intron5 intron17 C3orf23 PRKCD ENSG00000179152 ENSG00000163932 ENST00000342649 ENST00000394729 1 1 285343 5580 deletion somatic BWA-0.5.8 BRASS-0 19 2 24122611 PD4116a NCBI-37 3 44535985 + 3 65794269 + 1 C 0 Ensembl58 intergenic intron1 MAGI1 ENSG00000151276 ENST00000330909 -1 9223 deletion somatic BWA-0.5.8 BRASS-0 19 2 24122635 PD4116a NCBI-37 3 44546537 + 3 64605974 + 1 C 0 Ensembl58 intron1 intron19 ZNF852 ADAMTS9 ENSG00000178917 ENSG00000163638 ENST00000420423 ENST00000498707 -1 -1 56999 deletion somatic BWA-0.5.8 BRASS-0 14 2 HS2_5434:8:2:14747:145069 PD4116a NCBI-37 3 56323007 + 3 85674383 - 0 0 Ensembl58 intron3 intron1 ERC2 CADM2 ENSG00000187672 ENSG00000175161 ENST00000460849 ENST00000383699 -1 1 26059 253559 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 24125549 PD4116a NCBI-37 3 56442663 + 3 86760881 + 0 1 C Ensembl58 intron2 intergenic ERC2 ENSG00000187672 ENST00000460849 -1 26059 deletion somatic BWA-0.5.8 BRASS-0 21 2 HS2_5434:7:3:7662:141784 PD4116a NCBI-37 3 56449118 - 3 66066175 - 1 G 0 Ensembl58 intron2 intergenic ERC2 ENSG00000187672 ENST00000460849 -1 26059 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 5 4 24127802 PD4116a NCBI-37 3 64605107 - 3 65884782 + 0 0 Ensembl58 intron19 intron1 ADAMTS9 MAGI1 ENSG00000163638 ENSG00000151276 ENST00000498707 ENST00000330909 -1 -1 56999 9223 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 20 8 24128118 PD4116a NCBI-37 3 65781252 + 3 86386370 + 0 0 Ensembl58 intron1 intergenic MAGI1 ENSG00000151276 ENST00000330909 -1 9223 deletion somatic BWA-0.5.8 BRASS-0 8 2 24128160 PD4116a NCBI-37 3 65895231 + 3 86391436 + 1 T 0 Ensembl58 intron1 intergenic MAGI1 ENSG00000151276 ENST00000330909 -1 9223 deletion somatic BWA-0.5.8 BRASS-0 13 2 HS2_5434:6:8:14529:4981 PD4116a NCBI-37 3 66060330 - 3 85291762 + 5 TGCTT 0 Ensembl58 intergenic intron1 CADM2 ENSG00000175161 ENST00000407528 1 253559 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 HS2_5434:8:1:4543:169368 PD4116a NCBI-37 3 79560490 - 3 85291488 - 1 A 0 Ensembl58 intron2 intron1 ROBO1 CADM2 ENSG00000169855 ENSG00000175161 ENST00000464233 ENST00000407528 -1 1 6091 253559 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 24142717 PD4116a NCBI-37 3 83155410 + 3 86387740 + 1 T 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 13 2 HS2_5434:6:47:7224:198914 PD4116a NCBI-37 3 85293197 + 3 85295153 + 1 T 0 Ensembl58 intron1 intron1 CADM2 CADM2 ENSG00000175161 ENSG00000175161 ENST00000407528 ENST00000407528 1 1 253559 253559 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:6:65:21042:184255 PD4116a NCBI-37 3 85301557 + 3 86390437 - 0 0 Ensembl58 intron1 intergenic CADM2 ENSG00000175161 ENST00000407528 1 253559 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 HS2_5434:7:4:6393:125686 PD4116a NCBI-37 3 42329800 - 8 130789809 + 4 GCCC 0 Ensembl58 intergenic exon2 GSDMC ENSG00000147697 ENST00000276708 -1 56169 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 24200933 PD4116a NCBI-37 4 30376500 + 13 46109560 + 0 143 TAATAAATTATTATATCTTAATGTCTACATATGTATCATTTATCCACACATGCATTTTTTCCTAAAATTATCTCCACTAAGTACAATAATTCCTTCTAGTTAAAAAATTCTATGATTCTAACTAATGAAAGATTTAAAAATAC Ensembl58 intron7 3UTR ENSG00000237496 COG3 ENSG00000237496 ENSG00000136152 ENST00000424014 ENST00000349995 1 1 83548 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 HS2_5434:8:62:17997:66849/24207011 PD4116a NCBI-37 4 46612422 - 13 78386755 + 2 AA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 11 32 HS2_5434:8:48:10347:195309 PD4116a NCBI-37 4 138726220 + 4 138773114 + 2 AG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:6:41:15603:178798 PD4116a NCBI-37 4 64059349 + 4 64060648 + 2 CA 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:7:7:12839:136831/24298910 PD4116a NCBI-37 5 61444083 - 20 31613359 - 0 14 AAGAGCAATGCTGA Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 32 24318889 PD4116a NCBI-37 5 137742191 - 5 175899979 + 3 CAG 0 Ensembl58 intron11 intron1 KDM3B FAF2 ENSG00000120733 ENSG00000113194 ENST00000314358 ENST00000261942 1 1 51780 23197 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 15 8 HS2_5434:7:23:7792:69489 PD4116a NCBI-37 5 55829426 - 5 74902660 + 3 CAA 0 Ensembl58 intron3 intergenic ENSG00000225940 ENSG00000225940 ENST00000438651 -1 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 HS2_5434:8:48:19760:79257/24298738 PD4116a NCBI-37 5 60780783 - 5 61444400 - 1 A 0 Ensembl58 intron2 intergenic ZSWIM6 ENSG00000130449 ENST00000252744 1 57688 tandem_duplication somatic BWA-0.5.8 BRASS-0 38 4 HS2_5434:7:23:9883:25301 PD4116a NCBI-37 5 62705244 + 5 62709598 - 2 AC 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 7 1 24302803 PD4116a NCBI-37 5 73566918 - 5 77964644 - 2 TT 0 Ensembl58 intergenic intron3 LHFPL2 ENSG00000145685 ENST00000514587 -1 tandem_duplication somatic BWA-0.5.8 BRASS-0 18 4 24320990 PD4116a NCBI-37 5 146220636 + 6 21434660 + 3 TTG 0 Ensembl58 intron2 intergenic PPP2R2B ENSG00000156475 ENST00000504198 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 24 32 HS2_5434:8:25:2173:115280 PD4116a NCBI-37 6 82301248 + 20 53714591 - 2 TT 0 Ensembl58 intron1 intergenic FAM46A ENSG00000112773 ENST00000412306 -1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 24361823 PD4116a NCBI-37 6 120546515 - 6 136524220 - 1 G 0 Ensembl58 intergenic intron1 ENSG00000237596 ENSG00000237596 ENST00000417643 -1 tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 24367224 PD4116a NCBI-37 6 146079327 - 6 154328648 - 2 AT 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 24367465 PD4116a NCBI-37 6 147383045 + 6 155740471 + 2 GA 0 Ensembl58 intron5 intron10 ENSG00000233452 NOX3 ENSG00000233452 ENSG00000074771 ENST00000427394 ENST00000159060 -1 -1 50508 deletion somatic BWA-0.5.8 BRASS-0 9 2 HS2_5434:6:47:6890:185924 PD4116a NCBI-37 6 151516732 + 6 151533303 + 0 5 AACAT Ensembl58 intron1 intron1 ENSG00000223598 ENSG00000223598 ENSG00000223598 ENSG00000223598 ENST00000415477 ENST00000415477 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 6 2 HS2_5434:6:28:20282:17946 PD4116a NCBI-37 6 41370079 + 6 41383367 + 4 ATCT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 4 2 HS2_5434:7:24:2621:151968 PD4116a NCBI-37 6 85228815 + 6 85234690 + 5 ATTTC 0 Ensembl58 intron1 intron1 ENSG00000231776 ENSG00000231776 ENSG00000231776 ENSG00000231776 ENST00000454172 ENST00000454172 -1 -1 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:6:21:5895:159389 PD4116a NCBI-37 7 132453071 + 7 132467867 + 1 C 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:7:26:19917:74374 PD4116a NCBI-37 8 110368198 + 8 116231477 + 7 ACCAGAG 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 24446413 PD4116a NCBI-37 8 40262954 - 8 92378974 + 5 ATGTC 0 Ensembl58 intergenic intron14 SLC26A7 ENSG00000147606 ENST00000309536 1 115111 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 9 8 HS2_5434:6:46:17055:144440 PD4116a NCBI-37 8 73050578 + 8 73053126 + 2 CC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:6:2:19072:195774/24446215 PD4116a NCBI-37 8 39631444 - X 55758405 + 0 0 Ensembl58 intron11 intron6 ADAM2 RRAGB ENSG00000104755 ENSG00000083750 ENST00000265708 ENST00000262850 -1 1 2515 10325 interchromosomal somatic BWA-0.5.8 BRASS-0 40 32 24446407 PD4116a NCBI-37 8 40092255 + X 56807722 + 2 TT 0 Ensembl58 intergenic intron2 ENSG00000204272 ENSG00000204272 ENST00000451583 1 interchromosomal somatic BWA-0.5.8 BRASS-0 25 32 HS2_5434:6:68:6474:129537 PD4116a NCBI-37 9 120359410 - 13 45918061 + 3 GGC 0 Ensembl58 intergenic intron2 ENSG00000170919 ENSG00000170919 ENST00000405697 1 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 6 32 HS2_5434:7:65:7950:161976 PD4116a NCBI-37 9 120357912 + 17 31517511 + 3 AAA 0 Ensembl58 intergenic intron1 ACCN1 ENSG00000108684 ENST00000359872 -1 40 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 24530238 PD4116a NCBI-37 9 96567229 + 18 8272708 - 3 ATG 0 Ensembl58 intergenic intron17 PTPRM ENSG00000173482 ENST00000332175 1 5797 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 HS2_5434:8:46:7678:16426 PD4116a NCBI-37 X 19003856 + X 19005091 + 7 CCAGAAC 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 HS2_5434:6:8:16386:44623 PD4116a NCBI-37 X 30387620 + X 30396080 + 2 AT 0 Ensembl58 intergenic intergenic deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 HS2_5434:8:46:19572:31661 PD4116a NCBI-37 X 36473728 - X 86065853 - 0 4 TCAT Ensembl58 intergenic intron7 DACH2 ENSG00000126733 ENST00000373125 1 117154 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 4 4 36542576 PD4120a NCBI-37 1 110649913 - 1 112379883 - 0 0 Ensembl58 intergenic intron2 KCND3 ENSG00000171385 ENST00000302127 -1 3752 tandem_duplication somatic BWA-0.5.8 BRASS-0 4 36542403 PD4120a NCBI-37 1 105895635 - 22 29047137 - 2 AA 0 Ensembl58 intergenic intron1 TTC28 ENSG00000100154 ENST00000397906 -1 23331 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36623472 PD4120a NCBI-37 18 10011128 + 21 18651384 - 2 GG 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36623477 PD4120a NCBI-37 18 10174822 - 21 16607918 + 4 AGGA 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36624114 PD4120a NCBI-37 18 35563115 + 21 47973023 - 2 CT 0 Ensembl58 intergenic intron25 DIP2A ENSG00000160305 ENST00000417564 1 23181 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36556238 PD4120a NCBI-37 2 132949417 + 18 42706561 - 2 GC 0 Ensembl58 intron1 intergenic C21orf99 ENSG00000163046 ENST00000470729 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36556477 PD4120a NCBI-37 2 134742052 - 18 48372896 - 2 CT 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36556479 PD4120a NCBI-37 2 134749641 + 18 42718784 + 1 C 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36556833 PD4120a NCBI-37 2 152905692 + 18 51547071 + 2 TT 0 Ensembl58 intron2 intergenic CACNB4 ENSG00000182389 ENST00000427385 -1 785 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36556478 PD4120a NCBI-37 2 134743885 + 2 152998389 + 1 C 0 Ensembl58 intergenic intron7 STAM2 ENSG00000115145 ENST00000263904 -1 10254 deletion somatic BWA-0.5.8 BRASS-0 2 36556482 PD4120a NCBI-37 2 134760542 - 4 34758333 - 3 GAG 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36629240 PD4120a NCBI-37 21 32965167 - 21 46832536 - 0 0 Ensembl58 intergenic intron2 COL18A1 ENSG00000182871 ENST00000400347 1 tandem_duplication somatic BWA-0.5.8 BRASS-0 4 36568013 PD4120a NCBI-37 4 11251389 - 18 42727708 + 2 GT 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36568270 PD4120a NCBI-37 4 19716717 - 18 42705372 + 2 TA 0 Ensembl58 intron2 intergenic ENSG00000248515 ENSG00000248515 ENST00000511431 1 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36567559 PD4120a NCBI-37 4 2587839 + 18 51584965 - 1 G 0 Ensembl58 intron3 intergenic RNF4 ENSG00000063978 ENST00000508235 1 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36567973 PD4120a NCBI-37 4 9732107 - 18 38101602 + 4 GAAG 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36568271 PD4120a NCBI-37 4 19716644 + 21 32926455 + 4 CTGT 0 Ensembl58 intron2 intron1 ENSG00000248515 TIAM1 ENSG00000248515 ENSG00000156299 ENST00000511431 ENST00000286827 1 -1 7074 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36568285 PD4120a NCBI-37 4 20359301 - 21 19330738 + 1 T 0 Ensembl58 intron4 intron2 SLIT2 CHODL ENSG00000145147 ENSG00000154645 ENST00000504154 ENST00000400128 1 1 9353 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36568773 PD4120a NCBI-37 4 34206373 + 21 46780453 + 2 AT 0 Ensembl58 intron2 intergenic ENSG00000248685 ENSG00000248685 ENST00000514877 -1 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36568784 PD4120a NCBI-37 4 34756090 + 9 14476778 + 4 GTGC 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 32 36567814 PD4120a NCBI-37 4 8129085 - 9 14526088 - 0 2 AT Ensembl58 intron1 intergenic ABLIM2 ENSG00000163995 ENST00000428004 -1 84448 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36579245 PD4120a NCBI-37 6 3826823 - 18 232247 + 1 C 0 Ensembl58 intergenic intron11 THOC1 ENSG00000079134 ENST00000261600 -1 9984 interchromosomal somatic BWA-0.5.8 BRASS-0 32 36595607 PD4120a NCBI-37 9 14527790 - 21 35247320 - 3 AGA 0 Ensembl58 intergenic intron33 ITSN1 ENSG00000205726 ENST00000381318 1 6453 interchromosomal somatic BWA-0.5.8 BRASS-0 32 IL35_5185:5:53:6848:11749 PD4192a NCBI-37 1 26525138 - 1 31468425 + 1 A 0 Ensembl58 intron6 intron5 CATSPER4 PUM1 ENSG00000188782 ENSG00000134644 ENST00000338855 ENST00000426105 1 -1 378807 9698 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL35_5185:3:90:12520:8238 PD4192a NCBI-37 1 245641232 + 2 212161 - 0 0 Ensembl58 intron4 intergenic KIF26B ENSG00000162849 ENST00000407071 1 55083 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 4 32 IL35_5185:1:85:5217:14445 PD4192a NCBI-37 11 17862965 - 11 17866444 + 0 0 Ensembl58 intron10 intron10 SERGEF SERGEF ENSG00000129158 ENSG00000129158 ENST00000265965 ENST00000265965 -1 -1 26297 26297 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 26182256 PD4192a NCBI-37 17 37504933 + 17 37970402 - 3 AAT 0 Ensembl58 intron1 intron3 FBXL20 IKZF3 ENSG00000108306 ENSG00000161405 ENST00000264658 ENST00000346872 -1 -1 84961 22806 amplicon_associated somatic BWA-0.5.8 BRASS-0 44 1 IL35_5185:4:63:7800:17814 PD4192a NCBI-37 17 37885762 + 17 37886511 + 4 CCAG 0 Ensembl58 3UTR exon2 C17orf37 C17orf37 ENSG00000141741 ENSG00000141741 ENST00000394231 ENST00000394231 -1 -1 84299 84299 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 2 IL35_5185:4:116:14706:11490 PD4192a NCBI-37 17 38459016 + 17 38788329 + 3 AAT 0 Ensembl58 3UTR intron8 CDC6 SMARCE1 ENSG00000094804 ENSG00000073584 ENST00000209728 ENST00000348513 1 -1 990 6605 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 6 0 26183671 PD4192a NCBI-37 17 40111680 + 17 40668438 - 0 0 Ensembl58 intron6 intron20 TTC25 ATP6V0A1 ENSG00000204815 ENSG00000033627 ENST00000377540 ENST00000393829 1 1 535 amplicon_associated somatic BWA-0.5.8 BRASS-0 43 1 26183745 PD4192a NCBI-37 17 40656654 - 17 45487524 + 3 AGG 0 Ensembl58 intron17 intron21 ATP6V0A1 C17orf57 ENSG00000033627 ENSG00000178852 ENST00000264649 ENST00000331493 1 1 535 124989 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 53 8 26185677 PD4192a NCBI-37 17 49867362 + 17 49964898 - 1 G 0 Ensembl58 intron4 intron4 CA10 CA10 ENSG00000154975 ENSG00000154975 ENST00000285273 ENST00000285273 -1 -1 56934 56934 amplicon_associated somatic BWA-0.5.8 BRASS-0 31 1 IL35_5185:1:13:12606:11533 PD4192a NCBI-37 17 49872296 - 17 49969368 + 4 AACT 0 Ensembl58 intron4 intron4 CA10 CA10 ENSG00000154975 ENSG00000154975 ENST00000285273 ENST00000285273 -1 -1 56934 56934 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 5 8 25920208 PD4192a NCBI-37 2 44199062 - 11 17869551 - 2 TG 0 Ensembl58 intron11 intron10 LRPPRC SERGEF ENSG00000138095 ENSG00000129158 ENST00000260665 ENST00000265965 -1 -1 10128 26297 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 25915761 PD4192a NCBI-37 2 23840385 - 19 35655717 + 2 CT 0 Ensembl58 intron2 intron6 KLHL29 FXYD5 ENSG00000119771 ENSG00000089327 ENST00000489446 ENST00000392219 1 1 53827 interchromosomal somatic BWA-0.5.8 BRASS-0 3 32 IL35_5185:4:119:18091:10541 PD4192a NCBI-37 3 10909898 - 3 10911903 + 4 GACC 0 Ensembl58 intron5 intron5 SLC6A11 SLC6A11 ENSG00000132164 ENSG00000132164 ENST00000254488 ENST00000254488 1 1 6538 6538 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 4 8 IL35_5185:1:108:14779:15822 PD4192a NCBI-37 3 10922309 + 3 64330200 - 2 CC 0 Ensembl58 intron6 intergenic SLC6A11 ENSG00000132164 ENST00000254488 1 6538 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 25967688 PD4192a NCBI-37 3 143283929 - 3 145962444 + 3 GAG 0 Ensembl58 intron8 intron1 SLC9A9 PLSCR4 ENSG00000181804 ENSG00000114698 ENST00000316549 ENST00000383083 -1 -1 285195 57088 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 9 8 IL35_5185:4:81:8838:17721 PD4192a NCBI-37 3 26953077 + 3 158590133 - 0 29 GGTACATCACATTTGTACCGGGTACAAAG Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 25953738 PD4192a NCBI-37 3 53493428 - 3 110587858 - 2 AA 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 25945824 PD4192a NCBI-37 3 6248102 - 3 8356491 + 0 1 C Ensembl58 intron1 intron3 ENSG00000226022 ENSG00000227110 ENSG00000226022 ENSG00000227110 ENST00000435651 ENST00000420095 1 -1 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 8 8 IL35_5185:5:46:3779:9860 PD4192a NCBI-37 4 69732718 - 4 82910774 - 0 10 TAGTGAATCC Ensembl58 intergenic intron1 ENSG00000251331 ENSG00000251331 ENST00000508294 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL35_5185:1:79:6837:2988 PD4192a NCBI-37 4 78829712 - 4 96460166 + 2 AA 0 Ensembl58 intron6 intron1 MRPL1 UNC5C ENSG00000169288 ENSG00000182168 ENST00000315567 ENST00000453304 1 -1 65008 8633 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 5 8 25983393 PD4192a NCBI-37 4 79365922 + 4 80381834 + 0 11 GCTGTTAGATG Ensembl58 intron3 intergenic FRAS1 ENSG00000138759 ENST00000512123 1 deletion somatic BWA-0.5.8 BRASS-0 10 2 IL35_5185:4:82:12761:8673 PD4192a NCBI-37 4 82324631 - 4 83906867 - 2 GT 0 Ensembl58 intergenic intron1 LIN54 ENSG00000189308 ENST00000506560 -1 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL35_5185:3:84:2872:10027 PD4192a NCBI-37 4 82897713 + 4 82964020 - 0 12 ACATACCTGCAA Ensembl58 intron1 intron1 ENSG00000251331 ENSG00000251331 ENSG00000251331 ENSG00000251331 ENST00000512716 ENST00000512716 -1 -1 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 5 1 25984568 PD4192a NCBI-37 4 84167699 + 4 88106728 - 0 28 ATTTCTGTCCGTAAATAATTTTCGACTA Ensembl58 intron1 exon3 ENSG00000250057 KLHL8 ENSG00000250057 ENSG00000145332 ENST00000515670 ENST00000273963 -1 -1 57563 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 6 1 25983419 PD4192a NCBI-37 4 79501963 + 8 104947009 - 1 G 0 Ensembl58 intron4 intron12 ANXA3 RIMS2 ENSG00000138772 ENSG00000176406 ENST00000510502 ENST00000504942 1 1 9699 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 IL11_5184:4:35:10719:2452 PD4194a NCBI-37 17 28493048 - 17 39660230 + 0 0 Ensembl58 intron2 intron1 CCDC55 KRT13 ENSG00000126653 ENSG00000171401 ENST00000247026 ENST00000336861 1 -1 84081 3860 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 8 26272030 PD4194a NCBI-37 17 29081672 + 17 37669155 + 1 A 0 Ensembl58 intron3 intron8 ENSG00000247185 CDK12 ENSG00000247185 ENSG00000167258 ENST00000499895 ENST00000447079 1 1 51755 amplicon_associated somatic BWA-0.5.8 BRASS-0 37 2 26272613 PD4194a NCBI-37 17 32303017 + 17 38760723 - 3 TTA 0 Ensembl58 intron1 intergenic ACCN1 ENSG00000108684 ENST00000359872 -1 40 amplicon_associated somatic BWA-0.5.8 BRASS-0 3 1 26273702 PD4194a NCBI-37 17 37467537 - 17 37540521 + 0 0 Ensembl58 intron2 intron1 FBXL20 FBXL20 ENSG00000108306 ENSG00000108306 ENST00000264658 ENST00000264658 -1 -1 84961 84961 amplicon_associated somatic BWA-0.5.8 BRASS-0 30 8 IL11_5184:4:33:2593:13782 PD4194a NCBI-37 17 38118434 + 17 38924355 + 0 0 Ensembl58 intergenic intron6 KRT26 ENSG00000186393 ENST00000335552 -1 353288 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 2 26276453/IL11_5184:4:77:12429:12925 PD4194a NCBI-37 17 39990259 + 17 44801452 - 0 5 AATTG Ensembl58 intron4 intron15 NT5C3L NSF ENSG00000141698 ENSG00000073969 ENST00000393911 ENST00000398238 -1 1 115024 4905 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 29 6 1 26277063 PD4194a NCBI-37 17 44936757 + 17 46278441 + 1 A 0 Ensembl58 intron1 intron4 WNT9B SKAP1 ENSG00000158955 ENSG00000141293 ENST00000290015 ENST00000336915 1 -1 7484 8631 amplicon_associated somatic BWA-0.5.8 BRASS-0 12 2 IL34_5198:4:61:6340:10955 PD4198a NCBI-37 1 239813421 - 1 240054640 - 2 CA 0 Ensembl58 intron2 intron4 CHRM3 CHRM3 ENSG00000133019 ENSG00000133019 ENST00000255380 ENST00000255380 1 1 1131 1131 tandem_duplication somatic MAQ-0.7.1 capillary_sequencing 3 4 IL34_5198:1:112:10713:13727 PD4198a NCBI-37 11 67456290 + 11 69970790 - 3 GCC 0 Ensembl58 intergenic intron9 ANO1 ENSG00000131620 ENST00000355303 1 55107 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 26818520 PD4198a NCBI-37 11 67287569 - 22 44155069 + 2 GA 0 Ensembl58 exon4 intron5 CABP2 EFCAB6 ENSG00000167791 ENSG00000186976 ENST00000353903 ENST00000358439 -1 -1 51475 64800 interchromosomal somatic BWA-0.5.8 BRASS-0 16 32 26819583 PD4198a NCBI-37 11 71695026 + 22 45123618 - 1 T 0 Ensembl58 intron4 intron4 RNF121 PRR5 ENSG00000137522 ENSG00000186654 ENST00000361756 ENST00000336985 1 1 55298 55615 interchromosomal somatic BWA-0.5.8 BRASS-0 11 32 26839481/IL34_5198:1:18:15972:8980 PD4198a NCBI-37 12 49594575 + 12 66894258 + 4 GTCT 0 Ensembl58 intergenic intron7 GRIP1 ENSG00000155974 ENST00000398016 -1 23426 deletion somatic MAQ-0.7.1 capillary_sequencing 18 3 2 26837306 PD4198a NCBI-37 12 41308626 + 19 20289669 + 2 AG 0 Ensembl58 intron2 intron1 CNTN1 ZNF90 ENSG00000018236 ENSG00000213988 ENST00000347616 ENST00000335117 1 1 1272 90649 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 IL34_5198:4:32:13531:14287 PD4198a NCBI-37 13 69930177 + 13 69931327 + 0 1 A Ensembl58 intergenic intergenic head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 26861651/IL34_5198:4:4:14601:16837 PD4198a NCBI-37 13 83168583 - 16 73822944 - 3 TAT 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 11 3 32 26865886 PD4198a NCBI-37 13 111716874 - 18 34004243 - 1 T 0 Ensembl58 intergenic intron3 FHOD3 ENSG00000134775 ENST00000257209 1 80206 interchromosomal somatic BWA-0.5.8 BRASS-0 6 32 26899455 PD4198a NCBI-37 16 23597561 + 16 48555949 + 2 TC 0 Ensembl58 intron2 intergenic NDUFAB1 ENSG00000004779 ENST00000007516 -1 4706 deletion somatic BWA-0.5.8 BRASS-0 9 2 IL34_5198:3:5:8025:5443 PD4198a NCBI-37 16 2392725 - 16 19718306 + 2 GC 0 Ensembl58 intron1 exon5 ABCA17P C16orf88 ENSG00000238098 ENSG00000103550 ENST00000512848 ENST00000420899 1 -1 400506 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL34_5198:4:28:19505:8136 PD4198a NCBI-37 16 2409112 + 16 10227647 + 5 TGCAA 0 Ensembl58 intron1 intron2 ABCA17P GRIN2A ENSG00000238098 ENSG00000183454 ENST00000512848 ENST00000330684 1 -1 2903 deletion somatic MAQ-0.7.1 capillary_sequencing 3 2 IL34_5198:2:113:19016:13740 PD4198a NCBI-37 16 2594752 - 16 14622433 - 0 0 Ensembl58 intron1 intron21 PDPK1 PARN ENSG00000140992 ENSG00000140694 ENST00000268673 ENST00000437198 1 -1 5170 5073 tail_to_tail_inversion somatic MAQ-0.7.1 capillary_sequencing 3 8 IL34_5198:1:119:1161:17261 PD4198a NCBI-37 16 7073175 + 16 19689360 - 0 0 Ensembl58 intergenic intron27 C16orf62 ENSG00000103544 ENST00000251143 1 57020 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 4 1 IL34_5198:1:36:10528:6555 PD4198a NCBI-37 16 7090082 + 16 15839637 - 0 0 Ensembl58 intergenic intron20 MYH11 ENSG00000133392 ENST00000452625 -1 4629 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 6 1 IL34_5198:3:118:4225:12824 PD4198a NCBI-37 17 38369364 + 17 56478108 + 0 0 Ensembl58 intergenic intron2 RNF43 ENSG00000108375 ENST00000407977 -1 54894 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 2 IL34_5198:2:42:5881:14803 PD4198a NCBI-37 17 50250130 - 17 59902296 - 3 GTT 0 Ensembl58 intergenic intron6 BRIP1 ENSG00000136492 ENST00000259008 -1 83990 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 4 IL34_5198:2:60:17116:15539 PD4198a NCBI-37 17 50258157 + 17 60902669 - 2 TT 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 1 IL34_5198:2:66:14429:12897 PD4198a NCBI-37 17 51390797 + 17 51400469 + 1 A 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 2 26917842 PD4198a NCBI-37 17 52327136 - 17 54527859 + 2 TA 0 Ensembl58 intergenic intron10 ANKFN1 ENSG00000153930 ENST00000318698 1 162282 amplicon_associated somatic BWA-0.5.8 BRASS-0 16 8 26917947 PD4198a NCBI-37 17 52606231 - 17 61687809 + 2 TA 0 Ensembl58 intergenic intron14 KCNH6 ENSG00000173826 ENST00000392968 1 81033 amplicon_associated somatic BWA-0.5.8 BRASS-0 24 8 IL34_5198:1:92:13795:5832 PD4198a NCBI-37 17 53047432 + 17 55888656 + 0 0 Ensembl58 intron1 intergenic STXBP4 ENSG00000166263 ENST00000376352 1 252983 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 2 IL34_5198:1:1:14903:2847 PD4198a NCBI-37 17 54812815 - 17 55480769 + 2 CC 0 Ensembl58 intergenic intron5 MSI2 ENSG00000153944 ENST00000322684 1 124540 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 8 26920187 PD4198a NCBI-37 17 57435717 + 17 60879313 + 1 A 0 Ensembl58 intron2 intron1 YPEL2 Mar-10 ENSG00000175155 ENSG00000173838 ENST00000312655 ENST00000311269 1 -1 388403 162333 amplicon_associated somatic BWA-0.5.8 BRASS-0 25 2 IL34_5198:2:54:16728:8065 PD4198a NCBI-37 17 60981565 - 17 61023271 + 2 GC 0 Ensembl58 intergenic intergenic amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 8 IL34_5198:4:111:7417:13155 PD4198a NCBI-37 17 64625760 - 17 71433202 - 0 0 Ensembl58 intron3 intron8 PRKCA SDK2 ENSG00000154229 ENSG00000069188 ENST00000284384 ENST00000392650 1 -1 5578 54549 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 4 26919644 PD4198a NCBI-37 17 55891499 - 18 3550368 - 0 3 CCA Ensembl58 intergenic intron6 DLGAP1 ENSG00000170579 ENST00000400147 -1 9229 amplicon_associated somatic BWA-0.5.8 BRASS-0 13 32 IL34_5198:4:120:7827:3761 PD4198a NCBI-37 17 56697976 - 18 228606 + 0 0 Ensembl58 intron5 intron11 TEX14 THOC1 ENSG00000121101 ENSG00000079134 ENST00000349033 ENST00000261600 -1 -1 56155 9984 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_5198:2:117:3186:12099 PD4198a NCBI-37 17 58760288 + 18 3058737 - 2 TT 0 Ensembl58 intron1 intergenic BCAS3 ENSG00000141376 ENST00000390652 1 54828 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 8 32 26921591 PD4198a NCBI-37 17 61825948 - 18 14088351 + 0 0 Ensembl58 intron12 intergenic CCDC47 ENSG00000108588 ENST00000225726 -1 57003 amplicon_associated somatic BWA-0.5.8 BRASS-0 8 32 26922346 PD4198a NCBI-37 17 65294016 + 18 2716167 + 3 GTT 0 Ensembl58 intergenic intron17 ENSG00000101596 ENSG00000101596 ENST00000320876 1 23347 amplicon_associated somatic BWA-0.5.8 BRASS-0 43 32 IL34_5198:2:92:17779:4592 PD4198a NCBI-37 17 61701410 + 19 3956323 + 2 CT 0 Ensembl58 intron1 intergenic MAP3K3 ENSG00000198909 ENST00000361733 1 4215 amplicon_associated somatic MAQ-0.7.1 capillary_sequencing 4 32 IL34_5198:3:119:9205:19966 PD4198a NCBI-37 18 46622351 + 18 46623263 + 2 TG 0 Ensembl58 intron16 intron16 DYM DYM ENSG00000141627 ENSG00000141627 ENST00000269445 ENST00000269445 -1 -1 54808 54808 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 26942160/IL34_5198:1:68:10977:17832 PD4198a NCBI-37 19 21696504 + 19 23060892 + 1 G 0 Ensembl58 intron1 intergenic ZNF429 ENSG00000197013 ENST00000358491 1 353088 deletion somatic MAQ-0.7.1 capillary_sequencing 30 7 2 26415460 PD4198a NCBI-37 3 12367444 + 3 56679582 - 0 4 TTAA Ensembl58 intron2 intron14 PPARG C3orf63 ENSG00000132170 ENSG00000163946 ENST00000397010 ENST00000432540 1 -1 5468 23272 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 10 1 26418078 PD4198a NCBI-37 3 20401435 + 3 59153905 - 0 2 GG Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 6 1 IL34_5198:1:12:7370:3313 PD4198a NCBI-37 4 21650571 - 12 73865841 + 3 CTG 0 Ensembl58 intron1 intergenic KCNIP4 ENSG00000185774 ENST00000382152 -1 80333 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 8 32 IL34_5198:1:78:11621:4343 PD4198a NCBI-37 4 47740088 - 12 73876898 - 0 1 C Ensembl58 intron5 intergenic CORIN ENSG00000145244 ENST00000273857 -1 10699 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_5198:2:45:7371:8719 PD4198a NCBI-37 5 55125725 - 11 67296373 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_5198:3:44:7603:16707 PD4198a NCBI-37 5 55767962 + 11 70019451 - 0 0 Ensembl58 intron1 intron22 ENSG00000248727 ANO1 ENSG00000248727 ENSG00000131620 ENST00000506836 ENST00000355303 -1 1 55107 interchromosomal somatic MAQ-0.7.1 capillary_sequencing 3 32 IL34_5198:2:66:17845:5161 PD4198a NCBI-37 5 60300462 + 5 62184770 + 3 GGG 0 Ensembl58 intron1 intergenic NDUFAF2 ENSG00000164182 ENST00000296597 1 91942 deletion somatic MAQ-0.7.1 capillary_sequencing 5 2 26579199 PD4198a NCBI-37 5 62477579 + 5 63012762 + 0 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 13 2 IL34_5198:4:7:8571:9993 PD4198a NCBI-37 5 51180602 - X 27558985 - 0 20 CAATAACAATTTAGAAAAAT Ensembl58 intergenic intergenic interchromosomal somatic MAQ-0.7.1 capillary_sequencing 5 32 26573458 PD4198a NCBI-37 5 53568598 + X 41540611 + 3 AAA 0 Ensembl58 intron1 intron5 ARL15 CASK ENSG00000185305 ENSG00000147044 ENST00000332313 ENST00000442742 -1 -1 8573 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 IL34_5198:4:90:9480:10666 PD4198a NCBI-37 8 39638500 + 8 48097143 - 2 AG 0 Ensembl58 intron10 intergenic ADAM2 ENSG00000104755 ENST00000265708 -1 2515 head_to_head_inversion somatic MAQ-0.7.1 capillary_sequencing 3 1 26728817 PD4198a NCBI-37 8 48088723 - 8 60976607 + 1 T 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 5 8 33631346 PD4199a NCBI-37 1 52686225 - 1 58210637 - 0 0 Ensembl58 intron2 intron2 ZFYVE9 DAB1 ENSG00000157077 ENSG00000173406 ENST00000287727 ENST00000371236 1 -1 9372 1600 tandem_duplication somatic BWA-0.5.8 BRASS-0 5 4 33632186 PD4199a NCBI-37 1 55787787 - 1 57559533 - 0 0 Ensembl58 intergenic intron4 DAB1 ENSG00000173406 ENST00000371233 -1 1600 tandem_duplication somatic BWA-0.5.8 BRASS-0 14 4 33632194 PD4199a NCBI-37 1 55837587 - 1 57563937 + 0 0 Ensembl58 intergenic intron4 DAB1 ENSG00000173406 ENST00000371233 -1 1600 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 12 8 33632458 PD4199a NCBI-37 1 57545908 + 1 58727990 + 0 25 TAGCCCCTGGCAACTGTCACTTACT Ensembl58 intron3 intron4 DAB1 DAB1 ENSG00000173406 ENSG00000173406 ENST00000371234 ENST00000485760 -1 -1 1600 deletion somatic BWA-0.5.8 BRASS-0 15 2 34342715 PD4199a NCBI-37 14 39948730 - 14 46574136 - 0 0 Ensembl58 intergenic intergenic tandem_duplication somatic BWA-0.5.8 BRASS-0 9 4 34349681 PD4199a NCBI-37 14 54658083 - 14 74847077 + 1 A 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 7 8 34349752 PD4199a NCBI-37 14 54730454 + 14 70157936 + 0 3 TCA Ensembl58 intergenic intron2 KIAA0247 ENSG00000100647 ENST00000342745 1 9766 deletion somatic BWA-0.5.8 BRASS-0 18 2 34339283 PD4199a NCBI-37 14 33106803 + 18 10589533 - 1 T 0 Ensembl58 intron7 intergenic AKAP6 ENSG00000151320 ENST00000280979 1 9472 interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 34600850 PD4199a NCBI-37 20 6325419 + 20 32572980 + 3 TGG 0 Ensembl58 intergenic intron1 ENSG00000228265 ENSG00000228265 ENST00000432859 -1 deletion somatic BWA-0.5.8 BRASS-0 14 2 33762299 PD4199a NCBI-37 3 76194220 + 18 10453289 - 0 0 Ensembl58 intron1 intergenic ROBO2 ENSG00000185008 ENST00000403211 1 6092 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 33984505 PD4199a NCBI-37 8 124367606 - 8 128408083 + 1 A 0 Ensembl58 intron13 intron5 ATAD2 ENSG00000246228 ENSG00000156802 ENSG00000246228 ENST00000287394 ENST00000502082 -1 -1 29028 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 17 8 33972312 PD4199a NCBI-37 8 92311920 - 8 96087186 - 2 TA 0 Ensembl58 intron4 intron10 SLC26A7 C8orf38 ENSG00000147606 ENSG00000156170 ENST00000309536 ENST00000286687 1 1 115111 tandem_duplication somatic BWA-0.5.8 BRASS-0 6 4 34707442 PD4199a NCBI-37 X 116805795 + X 119236197 - 4 CAGC 0 Ensembl58 intergenic intron1 ENSG00000249999 ENSG00000249999 ENST00000504192 1 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 14 1 34694655 PD4199a NCBI-37 X 76744130 + X 104262815 + 1 A 0 Ensembl58 intergenic intron1 IL1RAPL2 ENSG00000189108 ENST00000344799 1 26280 deletion somatic BWA-0.5.8 BRASS-0 10 2 20773586 PD4248a NCBI-37 1 40828753 + 1 62887011 + 2 AA 0 Ensembl58 intron1 intergenic SMAP2 ENSG00000084070 ENST00000435168 1 deletion somatic BWA-0.5.8 BRASS-0 8 2 20773614 PD4248a NCBI-37 1 41071544 - 1 50072444 - 4 ACCT 0 Ensembl58 intergenic intron3 AGBL4 ENSG00000186094 ENST00000371839 -1 84871 tandem_duplication somatic BWA-0.5.8 BRASS-0 25 4 20773738 PD4248a NCBI-37 1 41766749 + 1 47657473 + 0 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 16 2 20768796 PD4248a NCBI-37 1 4337957 + 1 9873578 + 5 AAGAA 0 Ensembl58 intergenic intron1 CLSTN1 ENSG00000171603 ENST00000361311 -1 22883 deletion somatic BWA-0.5.8 BRASS-0 11 2 20773934 PD4248a NCBI-37 1 43893952 + 1 44482243 + 1 C 0 Ensembl58 exon13 intron2 KIAA0467 SLC6A9 ENSG00000198198 ENSG00000196517 ENST00000372442 ENST00000372310 1 -1 23334 6536 deletion somatic BWA-0.5.8 BRASS-0 8 2 20774640 PD4248a NCBI-37 1 49070289 - 1 107830375 + 2 AA 0 Ensembl58 intron9 intron2 AGBL4 NTNG1 ENSG00000186094 ENSG00000162631 ENST00000371839 ENST00000370068 -1 1 84871 22854 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 12 8 20775321 PD4248a NCBI-37 1 56348075 + 1 56471310 + 0 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 16 2 20775833 PD4248a NCBI-37 1 60429926 - 1 69083804 + 3 AAA 0 Ensembl58 intergenic intergenic tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 30 8 20775052 PD4248a NCBI-37 1 53386296 - 21 47552146 - 1 A 0 Ensembl58 intron1 exon28 ECHDC2 COL6A2 ENSG00000121310 ENSG00000142173 ENST00000358358 ENST00000300527 -1 1 55268 1292 interchromosomal somatic BWA-0.5.8 BRASS-0 7 32 20777520 PD4248a NCBI-37 1 71239088 + 21 43455105 - 0 0 Ensembl58 intron5 intergenic ENSG00000229051 ENSG00000229051 ENST00000419450 1 interchromosomal somatic BWA-0.5.8 BRASS-0 10 32 21008746 PD4248a NCBI-37 10 110026808 + 10 127487760 + 0 1 T Ensembl58 intergenic intron5 UROS ENSG00000188690 ENST00000368786 -1 7390 deletion somatic BWA-0.5.8 BRASS-0 25 2 21009422 PD4248a NCBI-37 10 124107825 + 10 130768293 - 1 C 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 26 1 20839976 PD4248a NCBI-37 2 140517782 - 2 141133864 - 2 TC 0 Ensembl58 intergenic intron68 LRP1B ENSG00000168702 ENST00000389484 -1 53353 tandem_duplication somatic BWA-0.5.8 BRASS-0 8 4 20872820 PD4248a NCBI-37 3 175463111 - 3 176370141 - 5 TCACT 0 Ensembl58 intron12 intron4 NAALADL2 ENSG00000232461 ENSG00000177694 ENSG00000232461 ENST00000454872 ENST00000428516 1 -1 254827 tandem_duplication somatic BWA-0.5.8 BRASS-0 8 4 20891929 PD4248a NCBI-37 4 69145130 - 21 44608233 - 0 0 Ensembl58 intergenic intergenic interchromosomal somatic BWA-0.5.8 BRASS-0 4 32 20927379 PD4248a NCBI-37 6 6675787 + 14 21062961 + 2 GC 0 Ensembl58 intergenic intron1 ENSG00000226910 ENSG00000226910 ENST00000415015 1 interchromosomal somatic BWA-0.5.8 BRASS-0 8 32 20927654 PD4248a NCBI-37 6 10561188 - 6 156334671 - 3 GAA 0 Ensembl58 intron1 intergenic GCNT2 ENSG00000111846 ENST00000316170 1 2651 tandem_duplication somatic BWA-0.5.8 BRASS-0 11 4 20929913 PD4248a NCBI-37 6 32947130 - 6 34283618 - 2 TG 0 Ensembl58 intron10 intron2 BRD2 NUDT3 ENSG00000204256 ENSG00000112664 ENST00000374831 ENST00000358797 1 -1 6046 11165 tandem_duplication somatic BWA-0.5.8 BRASS-0 17 4 20927233 PD4248a NCBI-37 6 5750165 - 6 157209357 - 0 0 Ensembl58 intron5 intron2 FARS2 ARID1B ENSG00000145982 ENSG00000049618 ENST00000324331 ENST00000275248 1 1 10667 57492 tandem_duplication somatic BWA-0.5.8 BRASS-0 11 4 20927234 PD4248a NCBI-37 6 5751792 + 6 156340268 - 2 CT 0 Ensembl58 intron5 intergenic FARS2 ENSG00000145982 ENST00000324331 1 10667 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 15 1 20933094 PD4248a NCBI-37 6 63527684 - 6 98659232 - 2 TA 0 Ensembl58 intergenic intron1 ENSG00000236920 ENSG00000236920 ENST00000418652 1 tandem_duplication somatic BWA-0.5.8 BRASS-0 16 4 20927356 PD4248a NCBI-37 6 6410741 + 6 66467500 + 1 C 0 Ensembl58 intron2 intergenic ENSG00000216863 ENSG00000216863 ENST00000447858 -1 deletion somatic BWA-0.5.8 BRASS-0 9 2 20933446 PD4248a NCBI-37 6 66452289 + 6 86667047 - 2 GG 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 8 1 20933845 PD4248a NCBI-37 6 70811631 - 6 109974500 + 0 0 Ensembl58 intron15 intron8 COL19A1 AKD1 ENSG00000082293 ENSG00000155085 ENST00000322773 ENST00000285397 1 -1 1310 221264 tail_to_tail_inversion somatic BWA-0.5.8 BRASS-0 10 8 20934271 PD4248a NCBI-37 6 74281127 + 6 89152410 - 0 0 Ensembl58 intergenic intergenic head_to_head_inversion somatic BWA-0.5.8 BRASS-0 5 1 20934705 PD4248a NCBI-37 6 76967913 + 6 86265299 - 4 CTGT 0 Ensembl58 intergenic intron6 SNX14 ENSG00000135317 ENST00000513869 -1 head_to_head_inversion somatic BWA-0.5.8 BRASS-0 20 1 20936361 PD4248a NCBI-37 6 89145188 + 6 98677519 + 0 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 6 2 20927567 PD4248a NCBI-37 6 9497098 + 6 98654941 + 2 AT 0 Ensembl58 intergenic intergenic deletion somatic BWA-0.5.8 BRASS-0 12 2 20975055 PD4248a NCBI-37 8 120558002 + 10 115944214 - 3 GAC 0 Ensembl58 intergenic intron1 TDRD1 ENSG00000095627 ENST00000251864 1 56165 interchromosomal somatic BWA-0.5.8 BRASS-0 24 32 20975378 PD4248a NCBI-37 8 126101969 + 10 123198397 + 0 1 T Ensembl58 intron1 intergenic KIAA0196 ENSG00000164961 ENST00000318410 -1 9897 interchromosomal somatic BWA-0.5.8 BRASS-0 12 32 20974201 PD4248a NCBI-37 8 109756017 + 8 113706870 + 0 0 Ensembl58 intergenic intron13 CSMD3 ENSG00000164796 ENST00000395717 -1 114788 deletion somatic BWA-0.5.8 BRASS-0 19 2