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 |