Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF02-EM02-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF02-EM02-Zygote_1_val_1.fq.gz -2 EF02-EM02-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 00:25:11 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF02-EM02-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 10,870,112 |
| Mapped reads | 10,870,112 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 10,870,112 / 100% |
| Mapped reads, first in pair | 5,435,056 / 50% |
| Mapped reads, second in pair | 5,435,056 / 50% |
| Mapped reads, both in pair | 10,870,112 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 86.07 |
| Overlapping read pairs | 5,427,314 / 99.86% |
| Duplicated reads (estimated) | 3,960,328 / 36.43% |
| Duplication rate | 42.63% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 357,720,748 / 38.28% |
| Number/percentage of C's | 108,200,706 / 11.58% |
| Number/percentage of T's | 361,704,085 / 38.7% |
| Number/percentage of G's | 106,948,695 / 11.44% |
| Number/percentage of N's | 5,754 / 0% |
| GC Percentage | 23.02% |
Coverage
| Mean | 1.3669 |
| Standard Deviation | 4.9 |
| Mean (paired-end reads overlap ignored) | 0.71 |
Mapping Quality
| Mean Mapping Quality | 17.36 |
Insert size
| Mean | 89 |
| Standard Deviation | 38.58 |
| P25/Median/P75 | 62 / 82 / 108 |
Mismatches and indels
| General error rate | 19.5% |
| Mismatches | 181,558,790 |
| Insertions | 670,714 |
| Mapped reads with at least one insertion | 5.97% |
| Deletions | 1,038,566 |
| Mapped reads with at least one deletion | 9.2% |
| Homopolymer indels | 45.1% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 105830214 | 1.6116 | 3.6873 |
| NC_035781.1 | 61752955 | 109673907 | 1.776 | 4.1474 |
| NC_035782.1 | 77061148 | 124121172 | 1.6107 | 3.8348 |
| NC_035783.1 | 59691872 | 105714655 | 1.771 | 3.7822 |
| NC_035784.1 | 98698416 | 183481338 | 1.859 | 4.2151 |
| NC_035785.1 | 51258098 | 49219995 | 0.9602 | 2.7765 |
| NC_035786.1 | 57830854 | 55045362 | 0.9518 | 2.6064 |
| NC_035787.1 | 75944018 | 74953819 | 0.987 | 2.7641 |
| NC_035788.1 | 104168038 | 89841425 | 0.8625 | 2.5865 |
| NC_035789.1 | 32650045 | 27578605 | 0.8447 | 2.6218 |
| NC_007175.2 | 17244 | 10480338 | 607.7672 | 341.9766 |
