Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

Meth1 (WGBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth8 (MBD) /Users/strigg/Desktop/20200416/Pact_C1/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth7 (MBD) /Users/strigg/Desktop/20200416/Pact_C1/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth4 (RRBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth4_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth2 (WGBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth6 (RRBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth6_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth3 (WGBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth5 (RRBS) /Users/strigg/Desktop/20200416/Pact_C1/Meth5_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth9 (MBD) /Users/strigg/Desktop/20200416/Pact_C1/Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats

Summary 

Globals

Number of samples 9
Number of groups 3
Total number of mapped reads 121,532,524
Mean samples coverage 1.01
Mean samples GC-content 28.33
Mean samples mapping quality 16.1
Mean samples insert size 77.44

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
Meth1 WGBS 0.0922 2.3086 27.12 12.9104 88.0
Meth2 WGBS 0.1569 3.2489 27.31 14.8507 82.0
Meth3 WGBS 0.1422 2.803 27.46 14.6502 99.0
Meth4 RRBS 0.691 171.7309 29.45 13.4068 33.0
Meth5 RRBS 1.4782 361.2867 29.51 15.2537 33.0
Meth6 RRBS 0.7944 176.6845 29.65 14.6711 33.0
Meth7 MBD 1.5936 8.5345 28.08 19.879 109.0
Meth8 MBD 2.8899 16.4916 28.55 19.9751 113.0
Meth9 MBD 1.2495 7.1047 27.87 19.2904 107.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 593460X) 

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 - 593460X)
  • 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
    • 2020/04/17 07:48:01
    Generated by QualiMap v.2.2.1