Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

Meth1 (WGBS) /Users/strigg/Desktop/20200416/Pact/Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth8 (MBD) /Users/strigg/Desktop/20200416/Pact/Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth7 (MBD) /Users/strigg/Desktop/20200416/Pact/Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth4 (RRBS) /Users/strigg/Desktop/20200416/Pact/Meth4_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth2 (WGBS) /Users/strigg/Desktop/20200416/Pact/Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth6 (RRBS) /Users/strigg/Desktop/20200416/Pact/Meth6_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth3 (WGBS) /Users/strigg/Desktop/20200416/Pact/Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth5 (RRBS) /Users/strigg/Desktop/20200416/Pact/Meth5_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth9 (MBD) /Users/strigg/Desktop/20200416/Pact/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 870,187,242
Mean samples coverage 29.8
Mean samples GC-content 21.72
Mean samples mapping quality 8.2
Mean samples insert size 127.67

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
Meth1 WGBS 10.2397 19.5008 20.33 9.5717 142.0
Meth2 WGBS 14.0862 25.6132 20.48 10.3851 134.0
Meth3 WGBS 11.6404 22.7718 20.51 9.664 138.0
Meth4 RRBS 53.7812 1723.6355 22.85 6.6588 120.0
Meth5 RRBS 108.1087 4226.3078 22.74 5.9966 123.0
Meth6 RRBS 50.8236 1694.5399 22.68 6.2613 122.0
Meth7 MBD 8.2088 43.9161 21.74 9.0185 122.0
Meth8 MBD 3.6914 31.5466 22.79 7.2764 128.0
Meth9 MBD 7.6429 31.0228 21.38 8.9272 120.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 961466X) 

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 - 961466X)
  • 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 07:43:34
    Generated by QualiMap v.2.2.1