Input data and parameters 

QualiMap command line

qualimap bamqc -bam data/output/test/genome/bamFileSort/SRR1039508.sort.bam -nw 400 -hm 3

Alignment

Command line: "/Users/xzh004/miniconda3/envs/rasflow/bin/hisat2-align-s --wrapper basic-0 -p 30 --known-splicesite-infile data/output/test/genome/splicesites.txt -x data/output/test/genome/indexes/index -S data/output/test/genome/samFile/SRR1039508.sam -1 /tmp/7363.inpipe1 -2 /tmp/7363.inpipe2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: hisat2 (2.1.0)
Analysis date: Tue Jan 14 21:43:15 PST 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: data/output/test/genome/bamFileSort/SRR1039508.sort.bam

Summary 

Globals

Reference size 10,000,000
Number of reads 95,722
Mapped reads 85,264 / 89.07%
Unmapped reads 10,458 / 10.93%
Mapped paired reads 85,264 / 89.07%
Mapped reads, first in pair 43,053 / 44.98%
Mapped reads, second in pair 42,211 / 44.1%
Mapped reads, both in pair 78,962 / 82.49%
Mapped reads, singletons 6,302 / 6.58%
Secondary alignments 3,754
Read min/max/mean length 63 / 63 / 65.47
Duplicated reads (estimated) 65,974 / 68.92%
Duplication rate 30.75%
Clipped reads 6,946 / 7.26%

ACGT Content

Number/percentage of A's 1,443,845 / 27.01%
Number/percentage of C's 1,620,331 / 30.31%
Number/percentage of T's 1,352,575 / 25.3%
Number/percentage of G's 929,536 / 17.39%
Number/percentage of N's 22,164,602 / 414.58%
GC Percentage 47.69%

Coverage

Mean 2.7512
Standard Deviation 22.8087

Mapping Quality

Mean Mapping Quality 7.91

Insert size

Mean 4,731.76
Standard Deviation 127,170.36
P25/Median/P75 114 / 141 / 183

Mismatches and indels

General error rate 0.21%
Mismatches 57,743
Insertions 223
Mapped reads with at least one insertion 0.26%
Deletions 1,008
Mapped reads with at least one deletion 1.18%
Homopolymer indels 97.16%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 10000000 27511906 2.7512 22.8087

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