/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Assembly: 2008/10/07 11:42:56
**      Project Directory: /pyrodata/Legionella/pneumoniae/130b/P_2008_10_07_11_42_10_runAssembly
**      Software Release: 1.1.03.24
**
***************************************************************************/

/*
**  Input information.
*/

runData
{
}

pairedReadData
{
	run
	{
		path = "/pyrodata01/2008_10_06_FLX1/R_2008_10_06_14_50_03_FLX10060109_Administrator_LPUENr1MVISr2/D_2008_10_06_18_51_32_FLX10060109_LPUENr1MVISr2_FullAnalysis";

		region
		{
			name                 = "1";
			sffFile              = "FH93HPE01.sff";
		numberOfReads = 305394, 246800;
		numberOfBases = 73241287, 38925511;
		numWithPairedRead = 65058;
		}

	}
}

/*
**  Operation metrics.
*/

runMetrics
{
	totalNumberOfReads = 248625; 
	totalNumberOfBases = 38942722; 

	numberSearches   = 29106;
	seedHitsFound    = 29820041, 1024.53;
	overlapsFound    = 832458, 28.60, 2.79%;
	overlapsReported = 797416, 27.40, 2.67%;
	overlapsUsed     = 519996, 17.87, 65.21%;
}

readAlignmentResults
{
}

pairedReadResults
{
	run
	{
		path = "/pyrodata01/2008_10_06_FLX1/R_2008_10_06_14_50_03_FLX10060109_Administrator_LPUENr1MVISr2/D_2008_10_06_18_51_32_FLX10060109_LPUENr1MVISr2_FullAnalysis";

		region
		{
			name                 = "1";
			sffFile              = "FH93HPE01.sff";
		numAlignedReads    = 243552, 65.74%;
		numAlignedBases    = 37637410, 51.39%;
		inferredReadError = 0.80%, 302080;

		numberWithBothMapped  = 59567;
		numWithOneUnmapped    = 2346;
		numWithMultiplyMapped = 2868;
		numWithBothUnmapped   = 277;
		}

	}
}

/*
** Consensus distribution information.
*/
consensusDistribution
{
	fullDistribution
	{
		signalBin =  0.0, 48567;
		signalBin =  0.5, 3;
		signalBin =  0.6, 4;
		signalBin =  0.7, 154;
		signalBin =  0.8, 32052;
		signalBin =  0.9, 1483876;
		signalBin =  1.0, 665506;
		signalBin =  1.1, 6171;
		signalBin =  1.2, 195;
		signalBin =  1.3, 25;
		signalBin =  1.4, 4;
		signalBin =  1.5, 9;
		signalBin =  1.6, 30;
		signalBin =  1.7, 1116;
		signalBin =  1.8, 53535;
		signalBin =  1.9, 427799;
		signalBin =  2.0, 170481;
		signalBin =  2.1, 6658;
		signalBin =  2.2, 251;
		signalBin =  2.3, 19;
		signalBin =  2.4, 1;
		signalBin =  2.5, 4;
		signalBin =  2.6, 45;
		signalBin =  2.7, 659;
		signalBin =  2.8, 13055;
		signalBin =  2.9, 91210;
		signalBin =  3.0, 76245;
		signalBin =  3.1, 7106;
		signalBin =  3.2, 324;
		signalBin =  3.3, 36;
		signalBin =  3.4, 3;
		signalBin =  3.5, 20;
		signalBin =  3.6, 180;
		signalBin =  3.7, 1738;
		signalBin =  3.8, 11395;
		signalBin =  3.9, 28653;
		signalBin =  4.0, 19005;
		signalBin =  4.1, 3299;
		signalBin =  4.2, 287;
		signalBin =  4.3, 28;
		signalBin =  4.4, 11;
		signalBin =  4.5, 36;
		signalBin =  4.6, 243;
		signalBin =  4.7, 1155;
		signalBin =  4.8, 3854;
		signalBin =  4.9, 7838;
		signalBin =  5.0, 6810;
		signalBin =  5.1, 2700;
		signalBin =  5.2, 635;
		signalBin =  5.3, 105;
		signalBin =  5.4, 17;
		signalBin =  5.5, 35;
		signalBin =  5.6, 115;
		signalBin =  5.7, 421;
		signalBin =  5.8, 1198;
		signalBin =  5.9, 2378;
		signalBin =  6.0, 2661;
		signalBin =  6.1, 1525;
		signalBin =  6.2, 421;
		signalBin =  6.3, 91;
		signalBin =  6.4, 28;
		signalBin =  6.5, 34;
		signalBin =  6.6, 143;
		signalBin =  6.7, 312;
		signalBin =  6.8, 633;
		signalBin =  6.9, 884;
		signalBin =  7.0, 752;
		signalBin =  7.1, 444;
		signalBin =  7.2, 148;
		signalBin =  7.3, 31;
		signalBin =  7.4, 25;
		signalBin =  7.5, 43;
		signalBin =  7.6, 95;
		signalBin =  7.7, 166;
		signalBin =  7.8, 211;
		signalBin =  7.9, 217;
		signalBin =  8.0, 110;
		signalBin =  8.1, 67;
		signalBin =  8.2, 18;
		signalBin =  8.3, 17;
		signalBin =  8.4, 12;
		signalBin =  8.5, 15;
		signalBin =  8.6, 7;
		signalBin =  8.7, 26;
		signalBin =  8.8, 27;
		signalBin =  8.9, 13;
		signalBin =  9.0, 14;
		signalBin =  9.1, 7;
		signalBin =  9.2, 4;
		signalBin =  9.3, 1;
		signalBin =  9.4, 1;
		signalBin =  9.6, 4;
		signalBin =  9.8, 1;
		signalBin = 10.0, 1;
		signalBin = 10.4, 1;
	}

	distributionPeaks
	{
		signalPeak = 1, 0.98;
		signalPeak = 2, 1.96;
		signalPeak = 3, 2.98;
		signalPeak = 4, 3.96;
		signalPeak = 5, 4.98;
		signalPeak = 6, 6.00;
		signalPeak = 7, 6.96;
		signalPeak = 8, 7.86;
	}

	thresholdsUsed
	{
		threshold = 0, 1, 0.48;
		threshold = 1, 2, 1.54;
		threshold = 2, 3, 2.46;
		threshold = 3, 4, 3.48;
		threshold = 4, 5, 4.44;
		threshold = 5, 6, 5.46;
		threshold = 6, 7, 6.48;
		threshold = 7, 8, 7.44;

		interpolationAmount = 0.99;
	}
}


/*
**  Consensus results.
*/
consensusResults
{
	readStatus
	{
		numberAssembled = 224840;
		numberPartial   = 10838;
		numberSingleton = 4614;
		numberRepeat    = 6488;
		numberOutlier   = 1845;
	}

	pairedReadStatus
	{
		numberWithBothMapped   = 59567;
		numberWithOneUnmapped  = 2346;
		numberMultiplyMapped   = 2868;
		numberWithBothUnmapped = 277;

		library
		{
			libraryName     = "454PairedRead";
			pairDistanceAvg = 3028.6;
			pairDistanceDev = 757.1;
		}
	}

	scaffoldMetrics
	{
		numberOfScaffolds   = 11;
		numberOfBases       = 3476886;

		avgScaffoldSize     = 316080;
		N50ScaffoldSize     = 2421541;
		largestScaffoldSize = 2421541;
	}

	largeContigMetrics
	{
		numberOfContigs   = 190;
		numberOfBases     = 3458697;

		avgContigSize     = 18203;
		N50ContigSize     = 35584;
		largestContigSize = 94398;

		Q40PlusBases      = 3422830, 98.96%;
		Q39MinusBases     = 35867, 1.04%;
	}

	allContigMetrics
	{
		numberOfContigs = 274;
		numberOfBases   = 3475018;
	}
}