/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Mapping: 2008/04/22 13:01:15
**      Project Directory: /remote/rigdata/nas11/ifx_projects_2007q2/C431/SV11042/L17_VIR_mapping
**      Software Release: 1.1.03.24
**
***************************************************************************/

/*
**  Input information.
*/

referenceSequenceData
{
	file
	{
		path = "/remote/rigdata/nas11/ifx_projects_2007q2/C431/SV11042/REFERENCE/Babesia_WGS.fna";
		numberOfReads = 13;
		numberOfBases = 8173701;
	}

}

runData
{
	file
	{
		path = "/remote/rigdata/it1/build10/R_2008_02_19_15_04_49_build10_dconners_100707593662420SV11042SID4669RunID24977732/D_2008_02_19_21_56_38_datarig42_AnalysisPipe/sff/E5R36BC01.sff";

		numberOfReads = 197656, 197654;
		numberOfBases = 45630140, 45600348;
	}

	file
	{
		path = "/remote/rigdata/it1/build10/R_2008_02_19_15_04_49_build10_dconners_100707593662420SV11042SID4669RunID24977732/D_2008_02_19_21_56_38_datarig42_AnalysisPipe/sff/E5R36BC02.sff";

		numberOfReads = 201522, 201520;
		numberOfBases = 46406978, 46377664;
	}

	file
	{
		path = "/remote/rigdata/it2/sc01/R_2008_04_02_15_33_38_sc01_jsalem_100707593660420SV11042SID4669RunID25129993/D_2008_04_02_23_03_54_d12_AnalysisPipe/sff/E766UCN01.sff";

		numberOfReads = 243841, 243841;
		numberOfBases = 53777529, 53772079;
	}

	file
	{
		path = "/remote/rigdata/it2/sc01/R_2008_04_02_15_33_38_sc01_jsalem_100707593660420SV11042SID4669RunID25129993/D_2008_04_02_23_03_54_d12_AnalysisPipe/sff/E766UCN02.sff";

		numberOfReads = 270298, 270298;
		numberOfBases = 61389804, 61384017;
	}

}

/*
**  Operation metrics.
*/

runMetrics
{
	numberOfReferenceSequences  = 13; 
	totalReferenceNumberOfBases = 8173701; 

	totalNumberOfReads = 908020; 
	totalNumberOfBases = 206894940; 

	numberSearches   = 908020;
	seedHitsFound    = 22625796, 24.92;
	overlapsFound    = 5879606, 6.48, 25.99%;
	overlapsReported = 1052246, 1.16, 4.65%;
	overlapsUsed     = 823029, 0.91, 78.22%;
}

readMappingResults
{
	file
	{
		path = "/remote/rigdata/it1/build10/R_2008_02_19_15_04_49_build10_dconners_100707593662420SV11042SID4669RunID24977732/D_2008_02_19_21_56_38_datarig42_AnalysisPipe/sff/E5R36BC01.sff";

		numMappedReads    = 191708, 96.99%;
		numMappedBases    = 43120146, 94.50%;
		inferredReadError = 2.75%, 1103685;
	}

	file
	{
		path = "/remote/rigdata/it1/build10/R_2008_02_19_15_04_49_build10_dconners_100707593662420SV11042SID4669RunID24977732/D_2008_02_19_21_56_38_datarig42_AnalysisPipe/sff/E5R36BC02.sff";

		numMappedReads    = 195538, 97.03%;
		numMappedBases    = 43875176, 94.54%;
		inferredReadError = 2.78%, 1138105;
	}

	file
	{
		path = "/remote/rigdata/it2/sc01/R_2008_04_02_15_33_38_sc01_jsalem_100707593660420SV11042SID4669RunID25129993/D_2008_04_02_23_03_54_d12_AnalysisPipe/sff/E766UCN01.sff";

		numMappedReads    = 234984, 96.37%;
		numMappedBases    = 50814836, 94.49%;
		inferredReadError = 2.74%, 1296041;
	}

	file
	{
		path = "/remote/rigdata/it2/sc01/R_2008_04_02_15_33_38_sc01_jsalem_100707593660420SV11042SID4669RunID25129993/D_2008_04_02_23_03_54_d12_AnalysisPipe/sff/E766UCN02.sff";

		numMappedReads    = 261563, 96.77%;
		numMappedBases    = 58041852, 94.55%;
		inferredReadError = 2.70%, 1462284;
	}

}

/*
** Consensus distribution information.
*/
consensusDistribution
{
	fullDistribution
	{
		signalBin =  0.0, 304287;
		signalBin =  0.6, 9;
		signalBin =  0.7, 225;
		signalBin =  0.8, 41368;
		signalBin =  0.9, 3456584;
		signalBin =  1.0, 701573;
		signalBin =  1.1, 8635;
		signalBin =  1.2, 512;
		signalBin =  1.3, 118;
		signalBin =  1.4, 34;
		signalBin =  1.5, 25;
		signalBin =  1.6, 57;
		signalBin =  1.7, 571;
		signalBin =  1.8, 43531;
		signalBin =  1.9, 797146;
		signalBin =  2.0, 228525;
		signalBin =  2.1, 4675;
		signalBin =  2.2, 917;
		signalBin =  2.3, 380;
		signalBin =  2.4, 175;
		signalBin =  2.5, 136;
		signalBin =  2.6, 285;
		signalBin =  2.7, 856;
		signalBin =  2.8, 17662;
		signalBin =  2.9, 178853;
		signalBin =  3.0, 63159;
		signalBin =  3.1, 1870;
		signalBin =  3.2, 600;
		signalBin =  3.3, 403;
		signalBin =  3.4, 270;
		signalBin =  3.5, 239;
		signalBin =  3.6, 354;
		signalBin =  3.7, 955;
		signalBin =  3.8, 9955;
		signalBin =  3.9, 43835;
		signalBin =  4.0, 14867;
		signalBin =  4.1, 645;
		signalBin =  4.2, 197;
		signalBin =  4.3, 170;
		signalBin =  4.4, 134;
		signalBin =  4.5, 109;
		signalBin =  4.6, 188;
		signalBin =  4.7, 537;
		signalBin =  4.8, 3122;
		signalBin =  4.9, 8185;
		signalBin =  5.0, 5052;
		signalBin =  5.1, 741;
		signalBin =  5.2, 103;
		signalBin =  5.3, 52;
		signalBin =  5.4, 48;
		signalBin =  5.5, 62;
		signalBin =  5.6, 78;
		signalBin =  5.7, 282;
		signalBin =  5.8, 994;
		signalBin =  5.9, 2018;
		signalBin =  6.0, 1330;
		signalBin =  6.1, 256;
		signalBin =  6.2, 29;
		signalBin =  6.3, 21;
		signalBin =  6.4, 22;
		signalBin =  6.5, 32;
		signalBin =  6.6, 88;
		signalBin =  6.7, 171;
		signalBin =  6.8, 296;
		signalBin =  6.9, 274;
		signalBin =  7.0, 144;
		signalBin =  7.1, 32;
		signalBin =  7.2, 11;
		signalBin =  7.3, 9;
		signalBin =  7.4, 10;
		signalBin =  7.5, 19;
		signalBin =  7.6, 37;
		signalBin =  7.7, 45;
		signalBin =  7.8, 46;
		signalBin =  7.9, 39;
		signalBin =  8.0, 15;
		signalBin =  8.1, 4;
		signalBin =  8.2, 4;
		signalBin =  8.3, 3;
		signalBin =  8.4, 6;
		signalBin =  8.5, 15;
		signalBin =  8.6, 10;
		signalBin =  8.7, 7;
		signalBin =  8.9, 2;
		signalBin =  9.3, 2;
		signalBin =  9.5, 4;
		signalBin =  9.7, 1;
		signalBin = 10.5, 1;
		signalBin = 11.2, 1;
		signalBin = 11.4, 1;
		signalBin = 12.1, 1;
	}

	distributionPeaks
	{
		signalPeak = 1, 0.96;
		signalPeak = 2, 1.96;
		signalPeak = 3, 2.96;
		signalPeak = 4, 3.94;
		signalPeak = 5, 4.96;
		signalPeak = 6, 5.94;
		signalPeak = 7, 6.88;
	}

	thresholdsUsed
	{
		threshold = 0, 1, 0.48;
		threshold = 1, 2, 1.50;
		threshold = 2, 3, 2.54;
		threshold = 3, 4, 3.52;
		threshold = 4, 5, 4.52;
		threshold = 5, 6, 5.40;
		threshold = 6, 7, 6.36;

		interpolationAmount = 0.98;
	}
}


/*
**  Consensus results.
*/
consensusResults
{
	readStatus
	{
		numberFullyMapped     = 735638, 80.55%;
		numberPartiallyMapped = 87391, 9.57%;
		numberUnmapped        = 24227, 2.65%;
		numberRepeat          = 60764, 6.65%;
	}

	largeContigMetrics
	{
		numberOfContigs   = 663;
		numberOfBases     = 7470086;

		avgContigSize     = 11267;
		N50ContigSize     = 53670;
		largestContigSize = 204799;

		Q40PlusBases      = 7310322, 97.86%;
		Q39MinusBases     = 159764, 2.14%;

		numUndercalls     = 161383;
		numOvercalls      = 157868;
		numHCUndercalls   = 84077;
		numHCOvercalls    = 104204;
		consensusAccuracy  = 95.7263%;
		HCconsensusAccuracy  = 97.4244%;
	}

	allContigMetrics
	{
		numberOfContigs = 1679;
		numberOfBases   = 7717905;
	}
}