/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Assembly: 2009/04/01 14:11:14
**      Project Directory: /lustre/pathogen/work/team81/jit/LEISH/Leishmania.010409
**      Software Release: 2.0.00.22
**
***************************************************************************/

/*
**  Input information.
*/

runData
{
	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H01.sff";

		numberOfReads = 33365, 33364;
		numberOfBases = 5654617, 5618382;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H02.sff";

		numberOfReads = 33598, 33594;
		numberOfBases = 5719527, 5678460;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H03.sff";

		numberOfReads = 35399, 35394;
		numberOfBases = 5877014, 5832651;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H04.sff";

		numberOfReads = 32537, 32532;
		numberOfBases = 5470105, 5430327;
	}

}

pairedReadData
{
	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FLVWW5T02.sff";

		numberOfReads = 264545, 376384;
		numberOfBases = 47295221, 37620112;
		numWithPairedRead = 120206;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FP8LRLE01.sff";

		numberOfReads = 87450, 134075;
		numberOfBases = 28604420, 23989998;
		numWithPairedRead = 51145;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FPJBGA001.sff";

		numberOfReads = 232477, 275412;
		numberOfBases = 58977049, 36185772;
		numWithPairedRead = 104252;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FQRGO9E01.sff";

		numberOfReads = 682686, 1059770;
		numberOfBases = 239566367, 202400321;
		numWithPairedRead = 412339;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FQRGO9E02.sff";

		numberOfReads = 497205, 768448;
		numberOfBases = 179962941, 151880807;
		numWithPairedRead = 298861;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FLVWW5T01.sff";

		numberOfReads = 430207, 658207;
		numberOfBases = 89519334, 71822221;
		numWithPairedRead = 239358;
	}

}

/*
**  Operation metrics.
*/

runMetrics
{
	totalNumberOfReads = 3407180; 
	totalNumberOfBases = 546459051; 

	numberSearches   = 227503;
	seedHitsFound    = 95314903, 418.96;
	overlapsFound    = 9317866, 40.96, 9.78%;
	overlapsReported = 8153860, 35.84, 8.55%;
	overlapsUsed     = 4150408, 18.24, 50.90%;
}

readAlignmentResults
{
	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H01.sff";

		numAlignedReads     = 33016, 98.96%;
		numAlignedBases     = 5112247, 90.99%;
		inferredReadError  = 1.51%, 77450;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H02.sff";

		numAlignedReads     = 33228, 98.91%;
		numAlignedBases     = 5163779, 90.94%;
		inferredReadError  = 1.51%, 78135;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H03.sff";

		numAlignedReads     = 35012, 98.92%;
		numAlignedBases     = 5292657, 90.74%;
		inferredReadError  = 1.54%, 81771;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FSGO63H04.sff";

		numAlignedReads     = 32161, 98.86%;
		numAlignedBases     = 4925853, 90.71%;
		inferredReadError  = 1.55%, 76135;
	}

}

pairedReadResults
{
	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FLVWW5T02.sff";

		numAlignedReads     = 366905, 97.48%;
		numAlignedBases     = 34996272, 93.03%;
		inferredReadError  = 1.52%, 532262;

		numberWithBothMapped  = 99533;
		numWithOneUnmapped    = 4498;
		numWithMultiplyMapped = 16054;
		numWithBothUnmapped   = 121;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FP8LRLE01.sff";

		numAlignedReads     = 132854, 99.09%;
		numAlignedBases     = 22804630, 95.06%;
		inferredReadError  = 0.85%, 193733;

		numberWithBothMapped  = 45795;
		numWithOneUnmapped    = 884;
		numWithMultiplyMapped = 4450;
		numWithBothUnmapped   = 16;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FPJBGA001.sff";

		numAlignedReads     = 270553, 98.24%;
		numAlignedBases     = 34084603, 94.19%;
		inferredReadError  = 1.11%, 379699;

		numberWithBothMapped  = 90031;
		numWithOneUnmapped    = 2550;
		numWithMultiplyMapped = 11423;
		numWithBothUnmapped   = 248;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FQRGO9E01.sff";

		numAlignedReads     = 1050035, 99.08%;
		numAlignedBases     = 192760591, 95.24%;
		inferredReadError  = 0.77%, 1482136;

		numberWithBothMapped  = 371254;
		numWithOneUnmapped    = 6756;
		numWithMultiplyMapped = 34181;
		numWithBothUnmapped   = 148;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FQRGO9E02.sff";

		numAlignedReads     = 759857, 98.88%;
		numAlignedBases     = 144632907, 95.23%;
		inferredReadError  = 0.72%, 1046480;

		numberWithBothMapped  = 269165;
		numWithOneUnmapped    = 5016;
		numWithMultiplyMapped = 24069;
		numWithBothUnmapped   = 611;
	}

	file
	{
		path = "/lustre/pathogen/work/team81/jit/LEISH/454_READS_SFF/FLVWW5T01.sff";

		numAlignedReads     = 643520, 97.77%;
		numAlignedBases     = 67118519, 93.45%;
		inferredReadError  = 1.24%, 830577;

		numberWithBothMapped  = 201736;
		numWithOneUnmapped    = 7791;
		numWithMultiplyMapped = 29611;
		numWithBothUnmapped   = 220;
	}

}

/*
** Consensus distribution information.
*/
consensusDistribution
{
	fullDistribution
	{
		signalBin =  0.0, 247134;
		signalBin =  0.1, 11;
		signalBin =  0.2, 7;
		signalBin =  0.3, 6;
		signalBin =  0.4, 8;
		signalBin =  0.5, 161131;
		signalBin =  0.6, 110669;
		signalBin =  0.7, 80650;
		signalBin =  0.8, 888853;
		signalBin =  0.9, 14697460;
		signalBin =  1.0, 7267417;
		signalBin =  1.1, 140475;
		signalBin =  1.2, 8124;
		signalBin =  1.3, 1872;
		signalBin =  1.4, 765;
		signalBin =  1.5, 955;
		signalBin =  1.6, 2692;
		signalBin =  1.7, 35166;
		signalBin =  1.8, 656673;
		signalBin =  1.9, 3006912;
		signalBin =  2.0, 1180682;
		signalBin =  2.1, 61514;
		signalBin =  2.2, 3541;
		signalBin =  2.3, 742;
		signalBin =  2.4, 494;
		signalBin =  2.5, 1291;
		signalBin =  2.6, 5941;
		signalBin =  2.7, 39327;
		signalBin =  2.8, 222582;
		signalBin =  2.9, 502371;
		signalBin =  3.0, 244633;
		signalBin =  3.1, 32253;
		signalBin =  3.2, 3496;
		signalBin =  3.3, 934;
		signalBin =  3.4, 1066;
		signalBin =  3.5, 3197;
		signalBin =  3.6, 9847;
		signalBin =  3.7, 30484;
		signalBin =  3.8, 72673;
		signalBin =  3.9, 98048;
		signalBin =  4.0, 67475;
		signalBin =  4.1, 20680;
		signalBin =  4.2, 4419;
		signalBin =  4.3, 1418;
		signalBin =  4.4, 1348;
		signalBin =  4.5, 2476;
		signalBin =  4.6, 4688;
		signalBin =  4.7, 9708;
		signalBin =  4.8, 19619;
		signalBin =  4.9, 29730;
		signalBin =  5.0, 21545;
		signalBin =  5.1, 6781;
		signalBin =  5.2, 1815;
		signalBin =  5.3, 1010;
		signalBin =  5.4, 1108;
		signalBin =  5.5, 1606;
		signalBin =  5.6, 2204;
		signalBin =  5.7, 3294;
		signalBin =  5.8, 4421;
		signalBin =  5.9, 5102;
		signalBin =  6.0, 4353;
		signalBin =  6.1, 2236;
		signalBin =  6.2, 997;
		signalBin =  6.3, 641;
		signalBin =  6.4, 701;
		signalBin =  6.5, 793;
		signalBin =  6.6, 1031;
		signalBin =  6.7, 1156;
		signalBin =  6.8, 1293;
		signalBin =  6.9, 1125;
		signalBin =  7.0, 843;
		signalBin =  7.1, 652;
		signalBin =  7.2, 520;
		signalBin =  7.3, 554;
		signalBin =  7.4, 586;
		signalBin =  7.5, 676;
		signalBin =  7.6, 744;
		signalBin =  7.7, 796;
		signalBin =  7.8, 767;
		signalBin =  7.9, 746;
		signalBin =  8.0, 753;
		signalBin =  8.1, 743;
		signalBin =  8.2, 730;
		signalBin =  8.3, 696;
		signalBin =  8.4, 724;
		signalBin =  8.5, 762;
		signalBin =  8.6, 722;
		signalBin =  8.7, 728;
		signalBin =  8.8, 674;
		signalBin =  8.9, 633;
		signalBin =  9.0, 679;
		signalBin =  9.1, 589;
		signalBin =  9.2, 588;
		signalBin =  9.3, 525;
		signalBin =  9.4, 476;
		signalBin =  9.5, 468;
		signalBin =  9.6, 438;
		signalBin =  9.7, 426;
		signalBin =  9.8, 431;
		signalBin =  9.9, 374;
		signalBin = 10.0, 295;
		signalBin = 10.1, 275;
		signalBin = 10.2, 292;
		signalBin = 10.3, 253;
		signalBin = 10.4, 238;
		signalBin = 10.5, 219;
		signalBin = 10.6, 191;
		signalBin = 10.7, 178;
		signalBin = 10.8, 165;
		signalBin = 10.9, 150;
		signalBin = 11.0, 122;
		signalBin = 11.1, 127;
		signalBin = 11.2, 109;
		signalBin = 11.3, 104;
		signalBin = 11.4, 84;
		signalBin = 11.5, 92;
		signalBin = 11.6, 63;
		signalBin = 11.7, 58;
		signalBin = 11.8, 54;
		signalBin = 11.9, 60;
		signalBin = 12.0, 43;
		signalBin = 12.1, 39;
		signalBin = 12.2, 43;
		signalBin = 12.3, 30;
		signalBin = 12.4, 47;
		signalBin = 12.5, 28;
		signalBin = 12.6, 28;
		signalBin = 12.7, 18;
		signalBin = 12.8, 23;
		signalBin = 12.9, 16;
		signalBin = 13.0, 19;
		signalBin = 13.1, 14;
		signalBin = 13.2, 11;
		signalBin = 13.3, 8;
		signalBin = 13.4, 15;
		signalBin = 13.5, 19;
		signalBin = 13.6, 7;
		signalBin = 13.7, 6;
		signalBin = 13.8, 3;
		signalBin = 13.9, 5;
		signalBin = 14.0, 6;
		signalBin = 14.1, 10;
		signalBin = 14.2, 6;
		signalBin = 14.3, 3;
		signalBin = 14.4, 6;
		signalBin = 14.5, 7;
		signalBin = 14.6, 4;
		signalBin = 14.7, 1;
		signalBin = 14.8, 3;
		signalBin = 15.0, 3;
		signalBin = 15.1, 2;
		signalBin = 15.2, 5;
		signalBin = 15.3, 1;
		signalBin = 15.4, 1;
		signalBin = 15.5, 2;
		signalBin = 15.6, 1;
		signalBin = 15.7, 1;
		signalBin = 16.0, 5;
		signalBin = 16.3, 1;
		signalBin = 16.4, 1;
		signalBin = 16.5, 1;
		signalBin = 16.6, 1;
		signalBin = 16.7, 1;
		signalBin = 16.9, 1;
		signalBin = 17.4, 3;
		signalBin = 18.4, 1;
		signalBin = 19.4, 1;
	}

	distributionPeaks
	{
		signalPeak = 1, 0.98;
		signalPeak = 2, 1.96;
		signalPeak = 3, 2.94;
		signalPeak = 4, 3.92;
		signalPeak = 5, 4.94;
		signalPeak = 6, 5.90;
		signalPeak = 7, 6.84;
		signalPeak = 8, 7.84;
		signalPeak = 9, 8.78;
		signalPeak = 10, 9.68;
		signalPeak = 11, 10.54;
		signalPeak = 12, 11.42;
	}

	thresholdsUsed
	{
		threshold = 0, 1, 0.28;
		threshold = 1, 2, 1.48;
		threshold = 2, 3, 2.40;
		threshold = 3, 4, 3.38;
		threshold = 4, 5, 4.38;
		threshold = 5, 6, 5.34;
		threshold = 6, 7, 6.32;
		threshold = 7, 8, 7.08;
		threshold = 8, 9, 8.30;
		threshold = 9, 10, 9.66;
		threshold = 10, 11, 10.20;
		threshold = 11, 12, 11.06;

		interpolationAmount = 0.98;
	}
}


/*
**  Consensus results.
*/
consensusResults
{
	readStatus
	{
		numAlignedReads    = 3357141, 98.53%;
		numAlignedBases    = 516892058, 94.59%;
		inferredReadError = 0.92%, 4778378;

		numberAssembled = 3049214;
		numberPartial   = 65827;
		numberSingleton = 50039;
		numberRepeat    = 237959;
		numberOutlier   = 4141;
		numberTooShort  = 0;
	}

	pairedReadStatus
	{
		numberWithBothMapped   = 1077514;
		numberWithOneUnmapped  = 27495;
		numberMultiplyMapped   = 119788;
		numberWithBothUnmapped = 1364;

		library
		{
			libraryName     = "FLVWW5T02.sff";
			pairDistanceAvg = 2915.3;
			pairDistanceDev = 728.8;
		}

		library
		{
			libraryName     = "FP8LRLE01.sff";
			pairDistanceAvg = 3151.3;
			pairDistanceDev = 787.8;
		}

		library
		{
			libraryName     = "FPJBGA001.sff";
			pairDistanceAvg = 3074.9;
			pairDistanceDev = 768.7;
		}

		library
		{
			libraryName     = "FQRGO9E01.sff";
			pairDistanceAvg = 3130.2;
			pairDistanceDev = 782.5;
		}

		library
		{
			libraryName     = "FQRGO9E02.sff";
			pairDistanceAvg = 3119.6;
			pairDistanceDev = 779.9;
		}

		library
		{
			libraryName     = "FLVWW5T01.sff";
			pairDistanceAvg = 2912.4;
			pairDistanceDev = 728.1;
		}
	}

	scaffoldMetrics
	{
		numberOfScaffolds   = 119;
		numberOfBases       = 30970487;

		avgScaffoldSize     = 260256;
		N50ScaffoldSize     = 561746;
		largestScaffoldSize = 2393801;
	}

	largeContigMetrics
	{
		numberOfContigs   = 5138;
		numberOfBases     = 29934682;

		avgContigSize     = 5826;
		N50ContigSize     = 10298;
		largestContigSize = 73993;

		Q40PlusBases      = 29630522, 98.98%;
		Q39MinusBases     = 304160, 1.02%;
	}

	allContigMetrics
	{
		numberOfContigs = 6765;
		numberOfBases   = 30371395;
	}
}