Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_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/SRR25787974_hisat2.sam -p 16 -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787974_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Feb 01 04:54:05 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam |
Summary
Globals
| Reference size | 4,411,532 |
| Number of reads | 26,007,427 |
| Mapped reads | 24,973,370 / 96.02% |
| Unmapped reads | 1,034,057 / 3.98% |
| Mapped paired reads | 24,973,370 / 96.02% |
| Mapped reads, first in pair | 12,480,857 / 47.99% |
| Mapped reads, second in pair | 12,492,513 / 48.03% |
| Mapped reads, both in pair | 24,640,558 / 94.74% |
| Mapped reads, singletons | 332,812 / 1.28% |
| Read min/max/mean length | 100 / 100 / 100 |
| Duplicated reads (estimated) | 22,971,571 / 88.33% |
| Duplication rate | 59.74% |
| Clipped reads | 2,403,304 / 9.24% |
ACGT Content
| Number/percentage of A's | 489,766,344 / 19.69% |
| Number/percentage of C's | 725,928,254 / 29.19% |
| Number/percentage of T's | 450,500,911 / 18.12% |
| Number/percentage of G's | 820,678,592 / 33% |
| Number/percentage of N's | 198,840,615,072 / 7995.6% |
| GC Percentage | 62.19% |
Coverage
| Mean | 45,636.6599 |
| Standard Deviation | 58,722.3625 |
Mapping Quality
| Mean Mapping Quality | 14.94 |
Insert size
| Mean | 25,281.12 |
| Standard Deviation | 227,105.98 |
| P25/Median/P75 | 134 / 166 / 199 |
Mismatches and indels
| General error rate | 0% |
| Mismatches | 3,371,174 |
| Insertions | 8,406 |
| Mapped reads with at least one insertion | 0.03% |
| Deletions | 69,895 |
| Mapped reads with at least one deletion | 0.28% |
| Homopolymer indels | 47.1% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| AL123456.3 | 4411532 | 201327585707 | 45,636.6599 | 58,722.3625 |
