Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

NI_2 (NI) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/NI_2
18h_3 (18h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/18h_3
18h (18h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/18h
NI_3 (NI) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/NI_3
NI (NI) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/NI
6h (6h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/6h
6h_2 (6h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/6h_2
6h_3 (6h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/6h_3
IR_3 (IR) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/IR_3
IR_2 (IR) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/IR_2
IR (IR) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/IR
18h_2 (18h) /data/qualimap_release_data/multisample_bamqc/gh2ax_chip_seq/18h_2

Summary 

Globals

Number of samples 12
Number of groups 4
Total number of mapped reads 406,459,903
Mean samples coverage 1.04
Mean samples GC-content 44.45
Mean samples mapping quality 32.3

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
18h 18h 0.76 4.5 42.65 32.21 0.0
18h_2 18h 1.29 3.78 49.18 32.26 0.0
18h_3 18h 0.86 4.23 42.94 32.26 0.0
6h 6h 0.89 5.51 42.18 32.26 0.0
6h_2 6h 1.16 4.01 48.28 32.23 0.0
6h_3 6h 1.06 5.25 42.55 32.39 0.0
NI NI 0.78 4.46 42.39 32.01 0.0
NI_2 NI 1.24 4.0 48.47 32.27 0.0
NI_3 NI 1.16 6.17 42.95 32.38 0.0
IR IR 0.91 5.54 41.07 32.35 0.0
IR_2 IR 1.35 4.51 47.97 32.5 0.0
IR_3 IR 1.0 4.67 42.75 32.52 0.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 17516X) 

Global Coverage Histogram 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped reads GC-content 

Mapped Reads Clipping Profile 

Mapped Reads GC-content Distribution 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Input data & parameters
  • Summary
  • PCA
  • Coverage Across Reference
  • Coverage Histogram (0 - 17516X)
  • Global Coverage Histogram
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped reads GC-content
  • Mapped Reads Clipping Profile
  • Mapped Reads GC-content Distribution
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2016/01/13 11:23:57
    Generated by QualiMap v.2.2-dev