Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_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/SRR25792493_hisat2.sam -p 16 -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25792493_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Feb 01 05:09:00 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam |
Summary
Globals
| Reference size | 4,411,532 |
| Number of reads | 29,615,840 |
| Mapped reads | 28,011,529 / 94.58% |
| Unmapped reads | 1,604,311 / 5.42% |
| Mapped paired reads | 28,011,529 / 94.58% |
| Mapped reads, first in pair | 14,001,270 / 47.28% |
| Mapped reads, second in pair | 14,010,259 / 47.31% |
| Mapped reads, both in pair | 27,702,476 / 93.54% |
| Mapped reads, singletons | 309,053 / 1.04% |
| Read min/max/mean length | 100 / 100 / 100 |
| Duplicated reads (estimated) | 25,655,585 / 86.63% |
| Duplication rate | 66.2% |
| Clipped reads | 2,863,411 / 9.67% |
ACGT Content
| Number/percentage of A's | 535,314,114 / 19.19% |
| Number/percentage of C's | 840,449,512 / 30.13% |
| Number/percentage of T's | 499,893,352 / 17.92% |
| Number/percentage of G's | 913,640,694 / 32.76% |
| Number/percentage of N's | 245,899,817,797 / 8815.83% |
| GC Percentage | 62.89% |
Coverage
| Mean | 56,372.5326 |
| Standard Deviation | 66,421.7922 |
Mapping Quality
| Mean Mapping Quality | 22.34 |
Insert size
| Mean | 15,901 |
| Standard Deviation | 178,012.71 |
| P25/Median/P75 | 133 / 164 / 201 |
Mismatches and indels
| General error rate | 0% |
| Mismatches | 3,635,014 |
| Insertions | 11,207 |
| Mapped reads with at least one insertion | 0.04% |
| Deletions | 84,271 |
| Mapped reads with at least one deletion | 0.3% |
| Homopolymer indels | 50.14% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| AL123456.3 | 4411532 | 248689231559 | 56,372.5326 | 66,421.7922 |
