Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

206 (Amb.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-206_S27_L004_dedup.sorted_stats
205 (Amb.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-205_S26_L004_dedup.sorted_stats
221 (Superlow.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-221_S33_L004_dedup.sorted_stats
220 (Superlow.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-220_S32_L004_dedup.sorted_stats
215 (Superlow.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-215_S31_L004_dedup.sorted_stats
227 (Amb.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-227_S35_L004_dedup.sorted_stats
226 (Amb.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-226_S34_L004_dedup.sorted_stats
214 (Superlow.low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/EPI-214_S30_L004_dedup.sorted_stats

Summary 

Globals

Number of samples 8
Number of groups 2
Total number of mapped reads 99,773,126
Mean samples coverage 1.19
Mean samples GC-content 24.07
Mean samples mapping quality 19.75
Mean samples insert size 132.12

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
205 Amb.low 0.9546 7.6143 24.17 19.7242 126.0
206 Amb.low 1.4107 11.1269 24.23 19.7052 129.0
220 Superlow.low 1.0003 8.4696 24.17 19.3246 132.0
221 Superlow.low 1.0548 8.3755 24.14 19.5521 133.0
214 Superlow.low 1.9679 12.3104 23.5 20.373 134.0
215 Superlow.low 1.3691 9.3638 24.03 19.9774 133.0
226 Amb.low 0.8226 7.1407 24.26 19.6401 137.0
227 Amb.low 0.9435 7.6315 24.08 19.6713 133.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 17300X) 

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 - 17300X)
  • 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
    • 2019/08/12 17:06:07
    Generated by QualiMap v.2.2.1