/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Assembly: 2012/02/28 16:39:46
**      Project Directory: /work/ng6/ergatis/output_repository/run_assembly_iterable/60_run_assembly/i1/g3
**      Software Release: 2.6 (20110517_1502)
**
***************************************************************************/

/*
**  Input information.
*/

runData
{
	file
	{
		path = "/work/ng6/ergatis/output_repository/pyrocleaner/60_pyrocleaner/i1/g6/MISE_2.107.decontaminated.clean.fasta";

		numberOfReads = 5043, 5041;
		numberOfBases = 2354189, 2297357;
	}

}

/*
**  Operation metrics.
*/

runMetrics
{
	inputFileNumReads  = 5043; 
	inputFileNumBases  = 2354189; 

	totalNumberOfReads = 5041; 
	totalNumberOfBases = 2297357; 

	numberSearches   = 458;
	seedHitsFound    = 197143, 430.44;
	overlapsFound    = 17738, 38.73, 9.00%;
	overlapsReported = 13590, 29.67, 76.62%;
	overlapsUsed     = 9696, 21.17, 71.35%;
}

readAlignmentResults
{
	file
	{
		path = "/work/ng6/ergatis/output_repository/pyrocleaner/60_pyrocleaner/i1/g6/MISE_2.107.decontaminated.clean.fasta";

		numAlignedReads     = 5005, 99.29%;
		numAlignedBases     = 2276127, 99.08%;
		inferredReadError  = 0.78%, 17764;
	}

}

/*
** Consensus distribution information.
*/
consensusDistribution
{
	fullDistribution
	{
		signalBin =  0.0, 3483;
		signalBin =  1.0, 24634;
		signalBin =  2.0, 7309;
		signalBin =  3.0, 2074;
		signalBin =  3.9, 1;
		signalBin =  4.0, 719;
		signalBin =  4.7, 1;
		signalBin =  4.8, 3;
		signalBin =  4.9, 9;
		signalBin =  5.0, 256;
		signalBin =  5.5, 1;
		signalBin =  5.7, 4;
		signalBin =  5.8, 8;
		signalBin =  5.9, 3;
		signalBin =  6.0, 79;
		signalBin =  6.8, 3;
		signalBin =  6.9, 4;
		signalBin =  7.0, 19;
		signalBin =  7.3, 1;
		signalBin =  7.7, 1;
		signalBin =  7.8, 6;
		signalBin =  7.9, 3;
		signalBin =  8.0, 3;
	}

	distributionPeaks
	{
		signalPeak = 1, 1.00;
		signalPeak = 2, 2.00;
		signalPeak = 3, 3.00;
		signalPeak = 4, 4.00;
	}

	thresholdsUsed
	{
		threshold = 0, 1, 0.50;
		threshold = 1, 2, 1.50;
		threshold = 2, 3, 2.50;
		threshold = 3, 4, 3.50;

		interpolationAmount = 1.00;
	}
}


/*
**  Alignment depths.
*/
alignmentDepths
{
	      1 = 0;
	      2 = 0;
	    3-4 = 0;
	    5-6 = 23;
	    7-8 = 106;
	   9-10 = 224;
	  11-13 = 222;
	  14-16 = 55;
	  17-19 = 80;
	  20-22 = 154;
	  23-25 = 467;
	  26-28 = 863;
	  29-31 = 1510;
	  32-34 = 3235;
	  35-38 = 7322;
	  39-42 = 10397;
	  43-46 = 9892;
	  47-50 = 8685;
	  51-55 = 7240;
	  56-60 = 3901;
	  61-70 = 3159;
	  71-80 = 999;
	  81-90 = 195;
	 91-100 = 0;
	101-140 = 0;
	141-180 = 0;
	181-240 = 0;
	241-300 = 0;
	301-400 = 0;
	401-500 = 0;
	501-600 = 0;
	601-700 = 0;
	701-850 = 0;
	851-1000 = 0;
	  1001+ = 0;

	peakDepth            = 41.0;
	estimatedGenomeSize  = "0.1 MB";
}

/*
**  Consensus results.
*/
consensusResults
{
	readStatus
	{
		numAlignedReads    = 5005, 99.29%;
		numAlignedBases    = 2276127, 99.08%;
		inferredReadError = 0.78%, 17764;

		numberAssembled = 4920;
		numberPartial   = 85;
		numberSingleton = 20;
		numberRepeat    = 0;
		numberOutlier   = 16;
		numberTooShort  = 0;
	}

	largeContigMetrics
	{
		numberOfContigs   = 1;
		numberOfBases     = 50562;

		avgContigSize     = 50562;
		N50ContigSize     = 50562;
		largestContigSize = 50562;

		Q40PlusBases      = 50531, 99.94%;
		Q39MinusBases     = 31, 0.06%;

		largeContigEndMetrics
		{
			NoEdges   = 0, 0.0%;
			OneEdge   = 2, 100.0%;
			TwoEdges  = 0, 0.0%;
			ManyEdges = 0, 0.0%;
		}
	}

	allContigMetrics
	{
		numberOfContigs = 1;
		numberOfBases   = 50562;
	}
}