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contributors:team_5:sspacesummaryfile2

EADING READS Lib1:


      Total inserted pairs = 1237731

READING READS Lib2:


      Total inserted pairs = 657883

CONTIG EXTENSION:


      Number of contig sequences =1450447
      Number of unmapped reads used for contig extension = 1146283
      Number of contigs extended = 11448
      Number of bases extended = 35147

LIBRARY Lib1 STATS:

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MAPPING READS TO CONTIGS:


      Number of single reads found on contigs = 942825
      Number of read-pairs used for pairing contigs / total pairs = 384640 / 384640

READ PAIRS STATS:

      Assembled pairs: 384640 (769280 sequences)
              Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 1500 +/-1500): 196624
              Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 53
              Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 24900
              Satisfied in distance/logic within a given contig pair (pre-scaffold): 120711
              Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 42352
      Total satisfied: 317335 unsatisfied: 67305
      Estimated insert size statistics (based on 196624 pairs):
              Mean insert size = 348
              Median insert size = 111

REPEATS:

      Number of repeated edges = 101

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LIBRARY Lib2 STATS:

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MAPPING READS TO CONTIGS:


      Number of single reads found on contigs = 596841
      Number of read-pairs used for pairing contigs / total pairs = 250690 / 250690

READ PAIRS STATS:

      Assembled pairs: 250690 (501380 sequences)
              Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 2000 +/-2000): 136202
              Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 22
              Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 14684
              Satisfied in distance/logic within a given contig pair (pre-scaffold): 77447
              Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 22335
      Total satisfied: 213649 unsatisfied: 37041
      Estimated insert size statistics (based on 136202 pairs):
              Mean insert size = 443
              Median insert size = 143

REPEATS:

      Number of repeated edges = 51

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SUMMARY:


      Inserted contig file;
              Total number of contigs = 1450447
              Sum (bp) = 2245788654
                      Total number of N's = 1255300
                      Sum (bp) no N's = 2244533354
              GC Content = 41.32%
              Max contig size = 153999
              Min contig size = 17
              Average contig size = 1548
              N25 = 17545
              N50 = 8429
              N75 = 3132
      After extension;
              Total number of contigs = 1450447
              Sum (bp) = 2245823801
                      Total number of N's = 1255300
                      Sum (bp) no N's = 2244568501
              GC Content = 41.32%
              Max contig size = 154009
              Min contig size = 17
              Average contig size = 1548
              N25 = 17545
              N50 = 8429
              N75 = 3132
      After scaffolding Lib1:
              Total number of scaffolds = 1448501
              Sum (bp) = 2246969737
                      Total number of N's = 2428590
                      Sum (bp) no N's = 2244541147
              GC Content = 41.32%
              Max scaffold size = 154009
              Min scaffold size = 17
              Average scaffold size = 1551
              N25 = 17609
              N50 = 8465
              N75 = 3143
      After scaffolding Lib2:
              Total number of scaffolds = 1446991
              Sum (bp) = 2248205142
                      Total number of N's = 3679315
                      Sum (bp) no N's = 2244525827
              GC Content = 41.32%
              Max scaffold size = 154009
              Min scaffold size = 17
              Average scaffold size = 1553
              N25 = 17673
              N50 = 8498
              N75 = 3156

Discussion

, 2015/05/27 09:45

It seems that the scaffolding is working and needs more mate pair data.

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contributors/team_5/sspacesummaryfile2.txt · Last modified: 2015/09/02 09:21 by ceisenhart