Input data and parameters 

QualiMap command line

qualimap bamqc -bam data/output/test/genome/bamFileSort/SRR1039509.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/SRR1039509.sam -1 /tmp/6026.inpipe1 -2 /tmp/6026.inpipe2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: hisat2 (2.1.0)
Analysis date: Tue Jan 14 21:42:36 PST 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: data/output/test/genome/bamFileSort/SRR1039509.sort.bam

Summary 

Globals

Reference size 10,000,000
Number of reads 96,432
Mapped reads 85,925 / 89.1%
Unmapped reads 10,507 / 10.9%
Mapped paired reads 85,925 / 89.1%
Mapped reads, first in pair 43,450 / 45.06%
Mapped reads, second in pair 42,475 / 44.05%
Mapped reads, both in pair 79,418 / 82.36%
Mapped reads, singletons 6,507 / 6.75%
Secondary alignments 2,852
Read min/max/mean length 63 / 63 / 64.86
Duplicated reads (estimated) 69,019 / 71.57%
Duplication rate 34.08%
Clipped reads 7,393 / 7.67%

ACGT Content

Number/percentage of A's 1,464,614 / 27.19%
Number/percentage of C's 1,645,211 / 30.55%
Number/percentage of T's 1,369,933 / 25.43%
Number/percentage of G's 906,410 / 16.83%
Number/percentage of N's 20,575,479 / 382.01%
GC Percentage 47.37%

Coverage

Mean 2.5963
Standard Deviation 23.7991

Mapping Quality

Mean Mapping Quality 10.07

Insert size

Mean 3,687.69
Standard Deviation 116,119.31
P25/Median/P75 115 / 142 / 186

Mismatches and indels

General error rate 0.23%
Mismatches 60,665
Insertions 244
Mapped reads with at least one insertion 0.28%
Deletions 1,101
Mapped reads with at least one deletion 1.28%
Homopolymer indels 97.32%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 10000000 25962762 2.5963 23.7991

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