Base Quality Distribution

Mean Base Quality

31

29

27

25 0

25

50

Position in read RG

ERR992655

75

100

Base Content Distribution ERR992655

Base Content Fraction

0.3

0.2

0.1

0.0 0

25

50

75

Position in read Base

A

C

G

N

T

100

Read Length Distribution

Fraction of reads

0.8

0.6

0.4

0.2

0.0 0

25

50

Read length RG

ERR992655

75

100

Mapping Quality Distribution

Fraction of reads

0.75

0.50

0.25

0.00 0

20

40

Mapping Quality RG

ERR992655

60

Coverage Distribution HG00513

Count

750,000,000

500,000,000

250,000,000

0 0

1

2

3

Coverage RG

ERR992655

4

5

Insert Size Distribution Insert size > 8166 (4.33%) Insert size < 2575 (0.97%) ERR992655 12,000

Layout HG00513

6,000

F− F+ R− R+

3,000

InsertSize

0 00 8,

0 00 6,

00

0

0

4,

Count

9,000

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

HG00513 ERR992655 0 0 565499 0.0144855 155603 0.00398584 38317868 0.981529 19207951 19109917 0.994896 175564 0.00458178 1445051 0.0377122 20326703 20166855 0.992136 18920808 0.930835 3216011937 173893355 3420663700 3405602459 0.995597 15061241 0.00440302 362844 0.000106074 311083 9.09423e−05 3564155 0.00104195 0 0 0.00564198 101 3 6624 1 0.306449 60

Base Quality Distribution - GitHub

ERR992655. 0. 25. 50. 75. 100. 0.0. 0.1. 0.2. 0.3. Position in read. Base Content Fraction. Base. A. C. G. N. T. Base Content Distribution ...

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