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
contributors/team_5/sspacesummaryfile2.txt · Last modified: 2015/09/02 16:21 by ceisenhart
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Discussion
It seems that the scaffolding is working and needs more mate pair data.