Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam -nw 400 -hm 3 |
Alignment
| Command line: | "/home/dguevara/pipeline/src/../tools/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -x ../mtuberculosis2/2-alignment/pathogen/indices/hisat2/mycobacteriumTuberculosis -S ../mtuberculosis2/2-alignment/pathogen/sam/mycobacteriumTuberculosis/SRR25792492_hisat2.sam -p 16 -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792492_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Feb 01 04:57:22 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam |
Summary
Globals
| Reference size | 4,411,532 |
| Number of reads | 33,108,733 |
| Mapped reads | 32,303,131 / 97.57% |
| Unmapped reads | 805,602 / 2.43% |
| Mapped paired reads | 32,303,131 / 97.57% |
| Mapped reads, first in pair | 16,175,687 / 48.86% |
| Mapped reads, second in pair | 16,127,444 / 48.71% |
| Mapped reads, both in pair | 32,010,043 / 96.68% |
| Mapped reads, singletons | 293,088 / 0.89% |
| Read min/max/mean length | 100 / 100 / 100 |
| Duplicated reads (estimated) | 29,839,540 / 90.13% |
| Duplication rate | 67.22% |
| Clipped reads | 2,577,527 / 7.79% |
ACGT Content
| Number/percentage of A's | 606,388,620 / 18.82% |
| Number/percentage of C's | 960,447,272 / 29.8% |
| Number/percentage of T's | 581,448,261 / 18.04% |
| Number/percentage of G's | 1,074,240,053 / 33.34% |
| Number/percentage of N's | 145,155,043,069 / 4504.39% |
| GC Percentage | 63.14% |
Coverage
| Mean | 33,634.0504 |
| Standard Deviation | 49,185.0032 |
Mapping Quality
| Mean Mapping Quality | 20.35 |
Insert size
| Mean | 12,383.42 |
| Standard Deviation | 159,883.39 |
| P25/Median/P75 | 150 / 182 / 215 |
Mismatches and indels
| General error rate | 0% |
| Mismatches | 4,385,814 |
| Insertions | 15,441 |
| Mapped reads with at least one insertion | 0.05% |
| Deletions | 90,396 |
| Mapped reads with at least one deletion | 0.28% |
| Homopolymer indels | 55.78% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| AL123456.3 | 4411532 | 148377689834 | 33,634.0504 | 49,185.0032 |
