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 |












