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 |