Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF08-CM03-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF08-CM03-Zygote_1_val_1.fq.gz -2 CF08-CM03-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 00:30:33 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF08-CM03-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 7,039,202 |
| Mapped reads | 7,039,202 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 7,039,202 / 100% |
| Mapped reads, first in pair | 3,519,601 / 50% |
| Mapped reads, second in pair | 3,519,601 / 50% |
| Mapped reads, both in pair | 7,039,202 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 92.09 |
| Overlapping read pairs | 3,512,728 / 99.8% |
| Duplicated reads (estimated) | 2,502,554 / 35.55% |
| Duplication rate | 39.3% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 261,870,646 / 40.45% |
| Number/percentage of C's | 60,723,607 / 9.38% |
| Number/percentage of T's | 264,997,312 / 40.93% |
| Number/percentage of G's | 59,832,385 / 9.24% |
| Number/percentage of N's | 4,041 / 0% |
| GC Percentage | 18.62% |
Coverage
| Mean | 0.9472 |
| Standard Deviation | 3.6343 |
| Mean (paired-end reads overlap ignored) | 0.5 |
Mapping Quality
| Mean Mapping Quality | 14.38 |
Insert size
| Mean | 96.49 |
| Standard Deviation | 42.37 |
| P25/Median/P75 | 66 / 89 / 119 |
Mismatches and indels
| General error rate | 14.94% |
| Mismatches | 96,046,578 |
| Insertions | 585,562 |
| Mapped reads with at least one insertion | 8.01% |
| Deletions | 867,818 |
| Mapped reads with at least one deletion | 11.77% |
| Homopolymer indels | 45.67% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 70898167 | 1.0796 | 3.3466 |
| NC_035781.1 | 61752955 | 72517995 | 1.1743 | 3.5479 |
| NC_035782.1 | 77061148 | 83140344 | 1.0789 | 3.4138 |
| NC_035783.1 | 59691872 | 71393054 | 1.196 | 3.5945 |
| NC_035784.1 | 98698416 | 121296667 | 1.229 | 3.7474 |
| NC_035785.1 | 51258098 | 35483088 | 0.6922 | 2.7675 |
| NC_035786.1 | 57830854 | 41237126 | 0.7131 | 2.7888 |
| NC_035787.1 | 75944018 | 54701324 | 0.7203 | 2.9874 |
| NC_035788.1 | 104168038 | 71873841 | 0.69 | 2.7 |
| NC_035789.1 | 32650045 | 21616314 | 0.6621 | 2.589 |
| NC_007175.2 | 17244 | 4427879 | 256.778 | 217.5205 |
