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Base Quality Distribution
Mean Base Quality
30
25
20
15 0
25
50
75
Position in read RG
ERR050082
ERR068361
SRR400038
SRR400039
100
Base Content Distribution ERR050082
ERR068361
SRR400038
SRR400039
Base Content Fraction
0.3 0.2 0.1 0.0
0.3 0.2 0.1 0.0 0
25
50
75
100
0
25
Position in read Base
A
C
G
N
T
50
75
100
Read Length Distribution
Fraction of reads
1.00
0.75
0.50
0.25
0.00 0
25
50
75
Read length RG
ERR050082
ERR068361
SRR400038
SRR400039
100
Mapping Quality Distribution
Fraction of reads
0.75
0.50
0.25
0.00 0
20
40
60
Mapping Quality RG
ERR050082
ERR068361
SRR400038
SRR400039
Coverage Distribution NA06985 500,000,000
Count
400,000,000
300,000,000
200,000,000
100,000,000
0 0
1
3
5
7
8
10
12
Coverage RG
ERR050082
ERR068361
SRR400038
SRR400039
14
16
Insert Size Distribution Insert size > 831 (11.98%) Insert size < 156 (0.44%) ERR050082
ERR068361
SRR400038
SRR400039
3,000,000
Layout 2,000,000
Count
NA06985
1,000,000
F− F+ R− R+
InsertSize
0 80
0 60
0 40
0 20
0 80
0 60
0 40
0 20
0 80
0 60
0 40
0 20
0 80
0 60
0 40
20
0
0
Sample Library #QCFail QCFailFraction #DuplicateMarked DuplicateFraction #Unmapped UnmappedFraction #Mapped MappedFraction #MappedRead1 #MappedRead2 RatioMapped2vsMapped1 #SecondaryAlignments SecondaryAlignmentFraction #SupplementaryAlignments SupplementaryAlignmentFraction #Pairs #MappedPairs MappedFraction #MappedSameChr MappedSameChrFraction #ReferenceBp #ReferenceNs #AlignedBases #MatchedBases MatchRate #MismatchedBases MismatchRate #DeletionsCigarD DeletionRate #InsertionsCigarI InsertionRate #SoftClippedBases SoftClipRate #HardClippedBases HardClipRate ErrorRate MedianReadLength DefaultLibraryLayout MedianInsertSize MedianCoverage SDCoverage MedianMAPQ
NA06985 SRR400039 0 0 2431204 0.00977714 1093849 0.00439894 245137001 0.985824 122869879 122267122 0.995094 3578267 0.014597 8972999 0.036604 130576303 129641649 0.992842 106683474 0.81702 3216700169 173893355 24249557863 24027309538 0.990835 222248325 0.00916505 3209151 0.000132339 2125617 8.76559e−05 26154469 0.00107855 0 0 0.0104636 101 2 349 8 0.340204 60
NA06985 SRR400038 0 0 1370415 0.0114318 1081555 0.00902218 117425436 0.979546 59161519 58263917 0.984828 1562045 0.0133024 4186877 0.0356556 62797390 61706651 0.982631 51125989 0.814142 3216700169 173893355 11439865089 11241195882 0.982634 198669207 0.0173664 1412772 0.000123496 1029203 8.99664e−05 13978289 0.00122189 0 0 0.0188017 100 2 348 4 0.320429 60
NA06985 ERR068361 0 0 897657 0.0095942 1520782 0.0162542 91144057 0.974152 45676305 45467752 0.995434 674414 0.00739943 3598217 0.0394784 48914962 47976665 0.980818 46127107 0.943006 3216700169 173893355 8976300240 8918470223 0.993557 57830017 0.00644252 999924 0.000111396 792792 8.83206e−05 6152364 0.000685401 0 0 0.00732764 100 2 493 3 0.341641 60
NA06985 ERR050082 0 0 754067 0.00892491 1545333 0.0182901 82190748 0.972785 41174957 41015791 0.996134 810858 0.00986556 3238496 0.0394022 44267679 43358636 0.979465 41725963 0.942583 3216700169 173893355 8057270066 7996763684 0.99249 60506382 0.00750954 1027379 0.00012751 753384 9.35036e−05 8295662 0.00102959 0 0 0.00876014 100 2 497 2 0.33387 60
Base Quality Distribution - GitHub
3216700169. 173893355. 24249557863. 24027309538. 0.990835. 222248325. 0.00916505. 3209151. 0.000132339. 2125617. 8.76559
e
â05. 26154469.
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