Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF03-EM03-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF03-EM03-Zygote_1_val_1.fq.gz -2 EF03-EM03-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 00:25:26 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF03-EM03-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 5,464,172 |
| Mapped reads | 5,464,172 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 5,464,172 / 100% |
| Mapped reads, first in pair | 2,732,086 / 50% |
| Mapped reads, second in pair | 2,732,086 / 50% |
| Mapped reads, both in pair | 5,464,172 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 91.35 |
| Overlapping read pairs | 2,727,092 / 99.82% |
| Duplicated reads (estimated) | 1,715,841 / 31.4% |
| Duplication rate | 37.7% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 197,378,137 / 39.59% |
| Number/percentage of C's | 51,118,498 / 10.25% |
| Number/percentage of T's | 199,685,956 / 40.05% |
| Number/percentage of G's | 50,377,070 / 10.1% |
| Number/percentage of N's | 4,078 / 0% |
| GC Percentage | 20.36% |
Coverage
| Mean | 0.7294 |
| Standard Deviation | 2.3045 |
| Mean (paired-end reads overlap ignored) | 0.38 |
Mapping Quality
| Mean Mapping Quality | 14.07 |
Insert size
| Mean | 95.43 |
| Standard Deviation | 41.56 |
| P25/Median/P75 | 66 / 88 / 117 |
Mismatches and indels
| General error rate | 15.78% |
| Mismatches | 78,205,858 |
| Insertions | 424,477 |
| Mapped reads with at least one insertion | 7.51% |
| Deletions | 650,072 |
| Mapped reads with at least one deletion | 11.38% |
| Homopolymer indels | 44.68% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 54101703 | 0.8239 | 2.1739 |
| NC_035781.1 | 61752955 | 57332493 | 0.9284 | 2.431 |
| NC_035782.1 | 77061148 | 65647618 | 0.8519 | 2.3281 |
| NC_035783.1 | 59691872 | 55526014 | 0.9302 | 2.3909 |
| NC_035784.1 | 98698416 | 96366255 | 0.9764 | 2.4592 |
| NC_035785.1 | 51258098 | 27100864 | 0.5287 | 1.8984 |
| NC_035786.1 | 57830854 | 31893168 | 0.5515 | 1.9017 |
| NC_035787.1 | 75944018 | 40749339 | 0.5366 | 1.7752 |
| NC_035788.1 | 104168038 | 52761443 | 0.5065 | 1.7761 |
| NC_035789.1 | 32650045 | 15637082 | 0.4789 | 1.6345 |
| NC_007175.2 | 17244 | 2317163 | 134.375 | 113.7094 |
