Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF01-EM01-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF01-EM01-Zygote_1_val_1.fq.gz -2 EF01-EM01-Zygote_2_val_2.fq.gz --genome BismarkIndex --bam --bowtie2 --multicore 4" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | yes |
| Program: | Bismark (v0.24.2) |
| Analysis date: | Thu Dec 05 00:25:32 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF01-EM01-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 6,795,976 |
| Mapped reads | 6,795,976 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 6,795,976 / 100% |
| Mapped reads, first in pair | 3,397,988 / 50% |
| Mapped reads, second in pair | 3,397,988 / 50% |
| Mapped reads, both in pair | 6,795,976 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 102.05 |
| Overlapping read pairs | 3,369,763 / 99.17% |
| Duplicated reads (estimated) | 1,971,830 / 29.01% |
| Duplication rate | 33.61% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 265,992,733 / 38.4% |
| Number/percentage of C's | 79,617,985 / 11.49% |
| Number/percentage of T's | 268,678,044 / 38.79% |
| Number/percentage of G's | 78,384,950 / 11.32% |
| Number/percentage of N's | 3,708 / 0% |
| GC Percentage | 22.81% |
Coverage
| Mean | 1.0132 |
| Standard Deviation | 3.9307 |
| Mean (paired-end reads overlap ignored) | 0.55 |
Mapping Quality
| Mean Mapping Quality | 13.77 |
Insert size
| Mean | 111.67 |
| Standard Deviation | 53.04 |
| P25/Median/P75 | 73 / 101 / 138 |
Mismatches and indels
| General error rate | 16.95% |
| Mismatches | 116,738,878 |
| Insertions | 576,354 |
| Mapped reads with at least one insertion | 8.16% |
| Deletions | 797,531 |
| Mapped reads with at least one deletion | 11.23% |
| Homopolymer indels | 42.93% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 74854940 | 1.1399 | 2.6485 |
| NC_035781.1 | 61752955 | 79623524 | 1.2894 | 2.9372 |
| NC_035782.1 | 77061148 | 90355794 | 1.1725 | 2.805 |
| NC_035783.1 | 59691872 | 77777205 | 1.303 | 2.8644 |
| NC_035784.1 | 98698416 | 131952019 | 1.3369 | 2.9579 |
| NC_035785.1 | 51258098 | 36496220 | 0.712 | 2.1786 |
| NC_035786.1 | 57830854 | 42436580 | 0.7338 | 2.0457 |
| NC_035787.1 | 75944018 | 56088776 | 0.7386 | 2.0597 |
| NC_035788.1 | 104168038 | 72692364 | 0.6978 | 2.11 |
| NC_035789.1 | 32650045 | 23528455 | 0.7206 | 2.0787 |
| NC_007175.2 | 17244 | 7986413 | 463.1416 | 380.2318 |
