Input data and parameters
QualiMap command line
| qualimap bamqc -bam zr3644_14.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 zr3644_14_R1_val_1_val_1_val_1.fq.gz -2 zr3644_14_R2_val_2_val_2_val_2.fq.gz --genome BismarkIndex --bam --bowtie2 --non_directional --multicore 2" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | yes |
| Program: | Bismark (v0.24.2) |
| Analysis date: | Tue Apr 01 02:03:10 GMT 2025 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | zr3644_14.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 563,985,803 |
| Number of reads | 23,667,126 |
| Mapped reads | 23,667,126 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 23,667,126 / 100% |
| Mapped reads, first in pair | 11,833,563 / 50% |
| Mapped reads, second in pair | 11,833,563 / 50% |
| Mapped reads, both in pair | 23,667,126 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 115 / 104.28 |
| Overlapping read pairs | 10,273,369 / 86.82% |
| Duplicated reads (estimated) | 3,081,576 / 13.02% |
| Duplication rate | 11.9% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 1,005,675,942 / 40.77% |
| Number/percentage of C's | 223,711,609 / 9.07% |
| Number/percentage of T's | 1,016,869,208 / 41.23% |
| Number/percentage of G's | 220,178,327 / 8.93% |
| Number/percentage of N's | 13,210 / 0% |
| GC Percentage | 18% |
Coverage
| Mean | 4.3767 |
| Standard Deviation | 6.5695 |
| Mean (paired-end reads overlap ignored) | 3.06 |
Mapping Quality
| Mean Mapping Quality | 24.92 |
Insert size
| Mean | 154.11 |
| Standard Deviation | 67.39 |
| P25/Median/P75 | 115 / 131 / 182 |
Mismatches and indels
| General error rate | 17.69% |
| Mismatches | 435,138,341 |
| Insertions | 1,073,462 |
| Mapped reads with at least one insertion | 4.43% |
| Deletions | 1,477,032 |
| Mapped reads with at least one deletion | 6.08% |
| Homopolymer indels | 51.78% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_088853.1 | 76070991 | 238273199 | 3.1322 | 6.8117 |
| NC_088854.1 | 61469542 | 324014708 | 5.2711 | 7.4406 |
| NC_088855.1 | 61039741 | 315200670 | 5.1639 | 6.3973 |
| NC_088856.1 | 57946171 | 219985476 | 3.7964 | 6.011 |
| NC_088857.1 | 57274926 | 285265338 | 4.9806 | 6.6913 |
| NC_088858.1 | 56905015 | 293137327 | 5.1513 | 6.5081 |
| NC_088859.1 | 53672946 | 291140975 | 5.4244 | 6.3999 |
| NC_088860.1 | 51133819 | 225374232 | 4.4075 | 6.4764 |
| NC_088861.1 | 50364239 | 149715192 | 2.9726 | 5.6049 |
| NC_088862.1 | 37310742 | 125185550 | 3.3552 | 6.1603 |
| NW_027062568.1 | 15579 | 40503 | 2.5998 | 4.0126 |
| NW_027062569.1 | 16498 | 11564 | 0.7009 | 2.3645 |
| NW_027062570.1 | 4000 | 17786 | 4.4465 | 5.0724 |
| NW_027062571.1 | 36893 | 0 | 0 | 0 |
| NW_027062572.1 | 51000 | 1495 | 0.0293 | 0.2192 |
| NW_027062573.1 | 2000 | 19937 | 9.9685 | 8.092 |
| NW_027062574.1 | 37061 | 1032 | 0.0278 | 0.2011 |
| NW_027062575.1 | 49428 | 80973 | 1.6382 | 4.0957 |
| NW_027062576.1 | 49232 | 79885 | 1.6226 | 4.5754 |
| NW_027062577.1 | 17087 | 31746 | 1.8579 | 2.8558 |
| NW_027062578.1 | 34507 | 270241 | 7.8315 | 6.8093 |
| NW_027062579.1 | 64000 | 87934 | 1.374 | 3.6115 |
| NW_027062580.1 | 24229 | 93364 | 3.8534 | 5.7061 |
| NW_027062581.1 | 5000 | 5441 | 1.0882 | 2.7634 |
| NW_027062582.1 | 18808 | 73741 | 3.9207 | 4.1814 |
| NW_027062583.1 | 1000 | 0 | 0 | 0 |
| NW_027062584.1 | 74000 | 1949 | 0.0263 | 0.318 |
| NW_027062585.1 | 39334 | 109751 | 2.7902 | 4.0713 |
| NW_027062586.1 | 258015 | 194369 | 0.7533 | 5.639 |
