Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF01-CM01-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF01-CM01-Zygote_1_val_1.fq.gz -2 CF01-CM01-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 00:28:51 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF01-CM01-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 1,297,078 |
| Mapped reads | 1,297,078 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 1,297,078 / 100% |
| Mapped reads, first in pair | 648,539 / 50% |
| Mapped reads, second in pair | 648,539 / 50% |
| Mapped reads, both in pair | 1,297,078 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 94.16 |
| Overlapping read pairs | 646,982 / 99.76% |
| Duplicated reads (estimated) | 409,492 / 31.57% |
| Duplication rate | 42.95% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 48,585,584 / 39.83% |
| Number/percentage of C's | 12,273,531 / 10.06% |
| Number/percentage of T's | 48,963,022 / 40.14% |
| Number/percentage of G's | 12,153,901 / 9.96% |
| Number/percentage of N's | 977 / 0% |
| GC Percentage | 20.03% |
Coverage
| Mean | 0.1784 |
| Standard Deviation | 0.7948 |
| Mean (paired-end reads overlap ignored) | 0.09 |
Mapping Quality
| Mean Mapping Quality | 15.68 |
Insert size
| Mean | 98.5 |
| Standard Deviation | 41.81 |
| P25/Median/P75 | 69 / 91 / 119 |
Mismatches and indels
| General error rate | 16.31% |
| Mismatches | 19,758,429 |
| Insertions | 111,362 |
| Mapped reads with at least one insertion | 8.26% |
| Deletions | 131,564 |
| Mapped reads with at least one deletion | 9.78% |
| Homopolymer indels | 44.85% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 13542754 | 0.2062 | 0.7704 |
| NC_035781.1 | 61752955 | 14006125 | 0.2268 | 0.8036 |
| NC_035782.1 | 77061148 | 15930537 | 0.2067 | 0.7616 |
| NC_035783.1 | 59691872 | 13636807 | 0.2285 | 0.8028 |
| NC_035784.1 | 98698416 | 23288595 | 0.236 | 0.8305 |
| NC_035785.1 | 51258098 | 6575680 | 0.1283 | 0.6332 |
| NC_035786.1 | 57830854 | 7460509 | 0.129 | 0.6172 |
| NC_035787.1 | 75944018 | 10068548 | 0.1326 | 0.6177 |
| NC_035788.1 | 104168038 | 12681151 | 0.1217 | 0.5973 |
| NC_035789.1 | 32650045 | 3997140 | 0.1224 | 0.602 |
| NC_007175.2 | 17244 | 969686 | 56.2332 | 39.0348 |
