Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples

Cdiff078_C40 /home/uzi/linuxTutorial/aln-pe.mapped.sorted.Cdiff078_C40_stats
Cdiff078_C41 /home/uzi/linuxTutorial/aln-pe.mapped.sorted.Cdiff078_C41_stats
Cdiff078_C42 /home/uzi/linuxTutorial/aln-pe.mapped.sorted.Cdiff078_C42_stats

Summary 

Globals

Number of samples 3

Sample name Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
Cdiff078_C40 2.1 11.71 28.9 1.69 534.0
Cdiff078_C41 0.66 6.72 29.68 0.65 535.0
Cdiff078_C42 2.0 11.83 28.7 1.68 527.0

PCA 

Coverage Across Reference 

Coverage Histogram (0-50X) 

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 (0-50X)
  • 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
    • 2015/01/23 22:17:11
    Generated by QualiMap v.2.0.1