Mean Base Quality

Base Quality Distribution

32

28

24

0

25

50

Position in read RG

SRR702072

75

100

Base Content Distribution SRR702072

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

1.00

0.75

0.50

0.25

0.00 0

25

50

Read length RG

SRR702072

75

100

Mapping Quality Distribution

Fraction of reads

0.75

0.50

0.25

0.00 0

20

40

Mapping Quality RG

SRR702072

60

Coverage Distribution HG00112 2,000,000,000

Count

1,500,000,000

1,000,000,000

500,000,000

0 0

28

56

85

113

141

Coverage RG

SRR702072

170

198

226

255

Insert Size Distribution Insert size > 436 (1.25%) Insert size < 103 (1.26%) SRR702072

200,000

Layout

100,000

F− F+ R− R+

50,000

InsertSize

0 40

0 30

0 20

0

0 10

Count

HG00112

150,000

Fraction of targets above coverage level

Target coverage distribution HG00112 1.00

0.75

0.50

0.25

0.00 0

50

100

150

Coverage Library

SRR702072

200

On−target rate HG00112

Fraction of reads on−target

1.00

0.75

0.50

0.25

0.00 0

100

200

300

Left/Right Extension of target region RG

SRR702072

400

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 #TotalBedBp #AlignedBasesInBed EnrichmentOverBed

HG00112 SRR702072 0 0 3415496 0.0543994 241904 0.00385286 59128126 0.941748 29602594 29525532 0.997397 58125 0.000983035 5486170 0.0927844 34153083 33950345 0.994064 32153003 0.941438 3214818421 173893355 5944863566 5928103588 0.997181 16759978 0.00281924 227551 3.82769e−05 154107 2.59227e−05 1898775 0.000319398 0 0 0.00320283 101 2 179 0 1.70956 60 32995992 2661629718 41.262

Base Quality Distribution - GitHub

SRR702072. 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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