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Old 06-30-2014, 06:31 PM   #15
pmart1
Junior Member
 
Location: Nashville

Join Date: Jun 2014
Posts: 8
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I was able to run it and these were the resulting metrics.

scaffoldMetrics
numberOfScaffolds = 51;
numberOfBases = 145548;
avgScaffoldSize = 2853;
N50ScaffoldSize = 2594, 19;
largestScaffoldSize = 12532;
numberOfScaffoldContigs = 51;
numberOfScaffoldContigBases = 145548;
avgScaffoldContigSize = 2853;
N50ScaffoldContigSize = 2594, 19;
largestScaffoldContigSize = 12532;
scaffoldEndMetrics
NoEdges = 97, 95.1%;
OneEdge = 1, 1.0%;
TwoEdges = 4, 3.9%;
ManyEdges = 0, 0.0%;
scaffoldGapMetrics
BothNoEdges = 0, 0.0%;
OneNoEdges = 0, 0.0%;
BothOneEdge = 0, 0.0%;
MultiEdges = 0, 0.0%;
largeContigMetrics
numberOfContigs = 2050;
numberOfBases = 1802379;
avgContigSize = 879;
N50ContigSize = 888;
largestContigSize = 12532;
Q40PlusBases = 1705911, 94.65%;
Q39MinusBases = 96468, 5.35%;
largeContigEndMetrics
NoEdges = 4052, 98.8%;
OneEdge = 29, 0.7%;
TwoEdges = 16, 0.4%;
ManyEdges = 3, 0.1%;
allContigMetrics
numberOfContigs = 4866;
numberOfBases = 2738478;
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