gene	contig	start	end	strand	length	SNPs	No. insertions	No. deletions	No. clipped regions	total insertion length	total deletion length	clipped length	No. contig breaks	Percent id	Match length	Match length percent	Overlapping secondary gene hits
repFIA	scaffold1|size4701254_part2	79	834	-	791	0	12	0	1	35	0	1	0	99.8735777497	790	99.8735777497	
mphR	scaffold1|size4701254_part34	1353	1938	-	612	0	9	0	1	26	0	1	0	99.8366013072	611	99.8366013072	
mphR	scaffold1|size4701254_part35	751	1336	+	612	0	9	0	1	26	0	1	0	99.8366013072	611	99.8366013072	
repFIA	scaffold1|size4701254_part42	2962	3717	-	791	0	12	0	1	35	0	1	0	99.8735777497	790	99.8735777497	
tetA	scaffold2|size436573_part1	775	2050	-	1343	0	21	0	1	67	0	1	0	99.9255398362	1342	99.9255398362