Input data and parameters 

QualiMap command line

qualimap bamqc -bam /data/qualimap_release_data/alignments/HG00096.chrom20.bam -c -nw 400 -hm 3

Alignment

BAM file: /data/qualimap_release_data/alignments/HG00096.chrom20.bam
Program: GATK IndelRealigner (1.0.4487)
Size of a homopolymer: 3
Number of windows: 400
Skip duplicated alignments: no
Analysis date: Wed Sep 02 09:28:03 CEST 2015
Draw chromosome limits: yes

Summary 

Globals

Reference size 63,025,520
Number of reads 2,939,810
Mapped reads 2,914,581 / 99.14%
Unmapped reads 25,229 / 0.86%
Paired reads 2,904,345 / 98.79%
Mapped reads, only first in pair 1,453,937 / 49.46%
Mapped reads, only second in pair 1,450,408 / 49.34%
Mapped reads, both in pair 2,896,042 / 98.51%
Mapped reads, singletons 8,303 / 0.28%
Read min/max/mean length 100 / 100 / 100
Clipped reads 678,220 / 23.07%
Duplicated reads (flagged) 39,111 / 1.33%

ACGT Content

Number/percentage of A's 78,482,215 / 28.24%
Number/percentage of C's 59,888,941 / 21.55%
Number/percentage of T's 79,422,510 / 28.58%
Number/percentage of G's 60,086,521 / 21.62%
Number/percentage of N's 0 / 0%
GC Percentage 43.18%

Coverage

Mean 4.41
Standard Deviation 2.75

Mapping Quality

Mean Mapping Quality 55.35

Insert size

Mean 3,128.51
Standard Deviation 295,452.44
P25/Median/P75 171 / 184 / 197

Mismatches and indels

General error rate 0.35%
Mismatches 938,327
Insertions 22,503
Mapped reads with at least one insertion 0.74%
Deletions 27,083
Mapped reads with at least one deletion 0.89%
Homopolymer indels 56.85%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
20 63025520 277945166 4.41 2.75

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapped Reads Clipping Profile 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram