Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

Meth15 (RRBS) /Users/strigg/Desktop/20200416/Mcap/Meth15_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth18 (MBD) /Users/strigg/Desktop/20200416/Mcap/Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth17 (MBD) /Users/strigg/Desktop/20200416/Mcap/Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth10 (WGBS) /Users/strigg/Desktop/20200416/Mcap/Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth11 (WGBS) /Users/strigg/Desktop/20200416/Mcap/Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth16 (MBD) /Users/strigg/Desktop/20200416/Mcap/Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth13 (RRBS) /Users/strigg/Desktop/20200416/Mcap/Meth13_R1_001_val_1_bismark_bt2_pe.sorted_stats
Meth12 (WGBS) /Users/strigg/Desktop/20200416/Mcap/Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
Meth14 (RRBS) /Users/strigg/Desktop/20200416/Mcap/Meth14_R1_001_val_1_bismark_bt2_pe.sorted_stats

Summary 

Globals

Number of samples 9
Number of groups 3
Total number of mapped reads 405,195,898
Mean samples coverage 5.85
Mean samples GC-content 21.81
Mean samples mapping quality 19.14
Mean samples insert size 139.44

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
Meth10 WGBS 3.1639 5.8352 21.51 18.1412 143.0
Meth11 WGBS 3.1567 6.1251 21.58 18.5587 148.0
Meth12 WGBS 4.8142 7.8004 21.32 18.0162 155.0
Meth13 RRBS 14.8044 138.1998 21.96 22.0539 150.0
Meth14 RRBS 9.3102 84.8473 22.46 22.2822 129.0
Meth15 RRBS 14.6337 116.3557 22.19 22.1085 137.0
Meth16 MBD 1.2581 3.2493 21.74 17.0336 135.0
Meth17 MBD 0.8427 2.267 21.84 16.9535 126.0
Meth18 MBD 0.681 1.794 21.68 17.1402 132.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 212008X) 

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 - 212008X)
  • 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 07:43:17
    Generated by QualiMap v.2.2.1