Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples

Collection_G0254FOG_1475.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0254FOG_1475.BWA_stats
Collection_G0256FOG_1498.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0256FOG_1498.BWA_stats
Collection_G0250FOG_1470.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0250FOG_1470.BWA_stats
Collection_G0089FOG_2060.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0089FOG_2060.BWA_stats
Collection_G0252FOG_1473.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0252FOG_1473.BWA_stats
Collection_G0092FOG_2063.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0092FOG_2063.BWA_stats
Collection_G0255FOG_1494.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0255FOG_1494.BWA_stats
Collection_G0253FOG_1474.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0253FOG_1474.BWA_stats
Collection_G0251FOG_1472.BWA.bam /home/genomics/rolbrechts/00_Data/01_First_analysis/00_Data/Collection_G0251FOG_1472.BWA_stats

Summary 

Globals

Number of samples 9
Total number of mapped reads 8,784,773
Mean samples coverage 35.14
Mean samples GC-content 40.31
Mean samples mapping quality 59.66

Sample statistics

Sample name Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
Collection_G0089FOG_2060.BWA.bam 25.4145 10.5951 40.71 59.5325 0.0
Collection_G0092FOG_2063.BWA.bam 30.079 12.6129 40.71 59.6406 0.0
Collection_G0250FOG_1470.BWA.bam 38.4949 10.237 40.25 59.6045 0.0
Collection_G0251FOG_1472.BWA.bam 36.2986 14.9508 40.41 59.6538 0.0
Collection_G0252FOG_1473.BWA.bam 39.9751 16.8614 39.85 59.6702 0.0
Collection_G0253FOG_1474.BWA.bam 39.422 14.8531 40.1 59.6799 0.0
Collection_G0254FOG_1475.BWA.bam 37.6343 17.3607 40.36 59.8345 0.0
Collection_G0255FOG_1494.BWA.bam 37.9973 13.3698 39.94 59.7006 0.0
Collection_G0256FOG_1498.BWA.bam 30.9002 10.1795 40.44 59.6146 0.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 134X) 

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 - 134X)
  • 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
    • 2023/06/09 15:42:47
    Generated by QualiMap v.2.2.1