Input data and parameters 

QualiMap command line

qualimap bamqc -bam data/output/test/genome/bamFileSort/SRR1039513.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/SRR1039513.sam -1 /tmp/6501.inpipe1 -2 /tmp/6501.inpipe2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: hisat2 (2.1.0)
Analysis date: Tue Jan 14 21:42:50 PST 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: data/output/test/genome/bamFileSort/SRR1039513.sort.bam

Summary 

Globals

Reference size 10,000,000
Number of reads 93,990
Mapped reads 81,910 / 87.15%
Unmapped reads 12,080 / 12.85%
Mapped paired reads 81,910 / 87.15%
Mapped reads, first in pair 41,034 / 43.66%
Mapped reads, second in pair 40,876 / 43.49%
Mapped reads, both in pair 75,756 / 80.6%
Mapped reads, singletons 6,154 / 6.55%
Secondary alignments 2,634
Read min/max/mean length 63 / 63 / 64.77
Duplicated reads (estimated) 61,553 / 65.49%
Duplication rate 30.07%
Clipped reads 7,081 / 7.53%

ACGT Content

Number/percentage of A's 1,406,778 / 27.38%
Number/percentage of C's 1,554,391 / 30.25%
Number/percentage of T's 1,305,699 / 25.41%
Number/percentage of G's 871,578 / 16.96%
Number/percentage of N's 24,552,248 / 477.81%
GC Percentage 47.21%

Coverage

Mean 2.9692
Standard Deviation 20.5994

Mapping Quality

Mean Mapping Quality 8.12

Insert size

Mean 6,132.1
Standard Deviation 171,235.95
P25/Median/P75 116 / 143 / 184

Mismatches and indels

General error rate 0.18%
Mismatches 52,981
Insertions 166
Mapped reads with at least one insertion 0.2%
Deletions 945
Mapped reads with at least one deletion 1.15%
Homopolymer indels 96.49%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 10000000 29691663 2.9692 20.5994

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