/***************************************************************************
**
**      454 Life Sciences Corporation
**         Newbler Metrics Results
**
**      Date of Mapping: 2011/09/13 18:13:12
**      Project Directory: /home/orf/ketan/Singhsir 18-08-2011/mid1
**      Software Release: 2.6 (20110517_1502)
**
***************************************************************************/

/*
**  Input information.
*/

referenceSequenceData
{
	file
	{
		path = "/media/ANAND/16s rRNA ecoli.fasta";
		numberOfReads = 1;
		numberOfBases = 1542;
	}

}

runData
{
	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_8F_534R.fasta";

		numberOfReads = 10776, 10776;
		numberOfBases = 2802251, 2802207;
	}

	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_517F_926R.fasta";

		numberOfReads = 2296, 2296;
		numberOfBases = 725624, 725617;
	}

	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_784F_1114R.fasta";

		numberOfReads = 1215, 1215;
		numberOfBases = 354836, 354831;
	}

}

/*
**  Operation metrics.
*/

runMetrics
{
	numberOfReferenceSequences  = 1; 
	totalReferenceNumberOfBases = 1542; 

	inputFileNumReads  = 14287; 
	inputFileNumBases  = 3882711; 

	totalNumberOfReads = 14287; 
	totalNumberOfBases = 3882655; 

	numberSearches   = 13785;
	seedHitsFound    = 42145, 3.06;
	overlapsFound    = 21251, 1.54, 50.42%;
	overlapsReported = 20711, 1.50, 97.46%;
	overlapsUsed     = 12332, 0.89, 59.54%;
}

readMappingResults
{
	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_8F_534R.fasta";

		numMappedReads     = 8925, 82.82%;
		numMappedBases     = 968249, 34.55%;
		inferredReadError  = 8.45%, 81845;
	}

	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_517F_926R.fasta";

		numMappedReads     = 2239, 97.52%;
		numMappedBases     = 272998, 37.62%;
		inferredReadError  = 8.08%, 22032;
	}

	file
	{
		path = "/home/orf/ketan/Singhsir 18-08-2011/Singhsir_amplicons/mid1out/mid1out_784F_1114R.fasta";

		numMappedReads     = 1168, 96.13%;
		numMappedBases     = 186820, 52.65%;
		inferredReadError  = 7.81%, 14585;
	}

}

/*
** Consensus distribution information.
*/
consensusDistribution
{
	fullDistribution
	{
		signalBin =  0.0, 345;
		signalBin =  1.0, 563;
		signalBin =  2.0, 172;
		signalBin =  3.0, 45;
		signalBin =  4.0, 5;
		signalBin =  4.4, 2;
		signalBin =  5.0, 2;
		signalBin =  5.3, 1;
	}

	distributionPeaks
	{
		signalPeak = 1, 1.00;
	}

	thresholdsUsed
	{
		threshold = 0, 1, 0.50;

		interpolationAmount = 1.00;
	}
}


/*
**  Consensus results.
*/
consensusResults
{
	readStatus
	{
		numMappedReads    = 12332, 86.32%;
		numMappedBases    = 1428067, 36.78%;
		inferredReadError = 8.30%, 118462;

		numberFullyMapped     = 0, 0.00%;
		numberPartiallyMapped = 5711, 39.97%;
		numberUnmapped        = 1453, 10.17%;
		numberRepeat          = 1, 0.01%;
		numberChimeric        = 6620, 46.34%;
		numberTooShort        = 502, 3.51%;
	}

	largeContigMetrics
	{
		numberOfContigs   = 1;
		numberOfBases     = 1125;

		avgContigSize     = 1125;
		N50ContigSize     = 1125;
		largestContigSize = 1125;

		Q40PlusBases      = 1021, 90.76%;
		Q39MinusBases     = 104, 9.24%;

		numUndercalls     = 66;
		numOvercalls      = 52;
		numHCUndercalls   = 41;
		numHCOvercalls    = 24;
		consensusAccuracy  = 89.5111%;
		HCconsensusAccuracy  = 93.6337%;
	}

	allContigMetrics
	{
		numberOfContigs = 2;
		numberOfBases   = 1231;
	}
}