Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_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/SRR25787976_hisat2.sam -p 16 -1 ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_1.fastq -2 ../mtuberculosis2/2-alignment/host/fastq/SRR25787976_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Feb 01 04:51:15 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam |
Summary
Globals
| Reference size | 4,411,532 |
| Number of reads | 33,341,480 |
| Mapped reads | 32,302,443 / 96.88% |
| Unmapped reads | 1,039,037 / 3.12% |
| Mapped paired reads | 32,302,443 / 96.88% |
| Mapped reads, first in pair | 16,162,819 / 48.48% |
| Mapped reads, second in pair | 16,139,624 / 48.41% |
| Mapped reads, both in pair | 32,027,228 / 96.06% |
| Mapped reads, singletons | 275,215 / 0.83% |
| Read min/max/mean length | 100 / 100 / 100 |
| Duplicated reads (estimated) | 30,043,140 / 90.11% |
| Duplication rate | 63.86% |
| Clipped reads | 2,667,928 / 8% |
ACGT Content
| Number/percentage of A's | 630,135,338 / 19.57% |
| Number/percentage of C's | 946,950,944 / 29.41% |
| Number/percentage of T's | 583,281,943 / 18.11% |
| Number/percentage of G's | 1,059,747,664 / 32.91% |
| Number/percentage of N's | 180,006,970,651 / 5590.08% |
| GC Percentage | 62.32% |
Coverage
| Mean | 41,533.6853 |
| Standard Deviation | 64,951.3363 |
Mapping Quality
| Mean Mapping Quality | 23.44 |
Insert size
| Mean | 10,824.18 |
| Standard Deviation | 146,498.52 |
| P25/Median/P75 | 139 / 169 / 199 |
Mismatches and indels
| General error rate | 0% |
| Mismatches | 3,546,495 |
| Insertions | 8,380 |
| Mapped reads with at least one insertion | 0.03% |
| Deletions | 69,331 |
| Mapped reads with at least one deletion | 0.21% |
| Homopolymer indels | 55.34% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| AL123456.3 | 4411532 | 183227181772 | 41,533.6853 | 64,951.3363 |
