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