Input data and parameters 

QualiMap command line

qualimap bamqc -bam data/output/test/genome/bamFileSort/SRR1039512.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/SRR1039512.sam -1 /tmp/6928.inpipe1 -2 /tmp/6928.inpipe2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: hisat2 (2.1.0)
Analysis date: Tue Jan 14 21:43:02 PST 2020
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: data/output/test/genome/bamFileSort/SRR1039512.sort.bam

Summary 

Globals

Reference size 10,000,000
Number of reads 99,424
Mapped reads 92,478 / 93.01%
Unmapped reads 6,946 / 6.99%
Mapped paired reads 92,478 / 93.01%
Mapped reads, first in pair 46,196 / 46.46%
Mapped reads, second in pair 46,282 / 46.55%
Mapped reads, both in pair 86,914 / 87.42%
Mapped reads, singletons 5,564 / 5.6%
Secondary alignments 2,369
Read min/max/mean length 63 / 63 / 64.5
Duplicated reads (estimated) 86,043 / 86.54%
Duplication rate 61.99%
Clipped reads 8,321 / 8.37%

ACGT Content

Number/percentage of A's 1,645,002 / 28.35%
Number/percentage of C's 1,824,224 / 31.44%
Number/percentage of T's 1,495,504 / 25.77%
Number/percentage of G's 838,032 / 14.44%
Number/percentage of N's 2,084,240 / 35.92%
GC Percentage 45.88%

Coverage

Mean 0.7888
Standard Deviation 30.7431

Mapping Quality

Mean Mapping Quality 4.82

Insert size

Mean 1,996.39
Standard Deviation 67,562.41
P25/Median/P75 120 / 150 / 197

Mismatches and indels

General error rate 0.89%
Mismatches 70,331
Insertions 73
Mapped reads with at least one insertion 0.08%
Deletions 1,145
Mapped reads with at least one deletion 1.24%
Homopolymer indels 98.77%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
1 10000000 7888155 0.7888 30.7431

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