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 |