Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF02-CM02-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF02-CM02-Zygote_1_val_1.fq.gz -2 CF02-CM02-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: | CF02-CM02-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 6,565,986 |
| Mapped reads | 6,565,986 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 6,565,986 / 100% |
| Mapped reads, first in pair | 3,282,993 / 50% |
| Mapped reads, second in pair | 3,282,993 / 50% |
| Mapped reads, both in pair | 6,565,986 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 89.95 |
| Overlapping read pairs | 3,278,341 / 99.86% |
| Duplicated reads (estimated) | 2,410,088 / 36.71% |
| Duplication rate | 41.11% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 238,697,109 / 40.47% |
| Number/percentage of C's | 55,223,739 / 9.36% |
| Number/percentage of T's | 241,599,242 / 40.96% |
| Number/percentage of G's | 54,318,289 / 9.21% |
| Number/percentage of N's | 3,238 / 0% |
| GC Percentage | 18.57% |
Coverage
| Mean | 0.863 |
| Standard Deviation | 3.316 |
| Mean (paired-end reads overlap ignored) | 0.45 |
Mapping Quality
| Mean Mapping Quality | 13.69 |
Insert size
| Mean | 93.04 |
| Standard Deviation | 38.23 |
| P25/Median/P75 | 66 / 87 / 114 |
Mismatches and indels
| General error rate | 14.44% |
| Mismatches | 84,598,451 |
| Insertions | 522,751 |
| Mapped reads with at least one insertion | 7.7% |
| Deletions | 786,461 |
| Mapped reads with at least one deletion | 11.48% |
| Homopolymer indels | 44.73% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 64290067 | 0.979 | 3.3371 |
| NC_035781.1 | 61752955 | 65690499 | 1.0638 | 3.379 |
| NC_035782.1 | 77061148 | 76763476 | 0.9961 | 3.4483 |
| NC_035783.1 | 59691872 | 64420494 | 1.0792 | 3.495 |
| NC_035784.1 | 98698416 | 110455912 | 1.1191 | 3.5877 |
| NC_035785.1 | 51258098 | 32812140 | 0.6401 | 2.7725 |
| NC_035786.1 | 57830854 | 37518210 | 0.6488 | 2.8299 |
| NC_035787.1 | 75944018 | 48905423 | 0.644 | 2.7062 |
| NC_035788.1 | 104168038 | 67342652 | 0.6465 | 2.7243 |
| NC_035789.1 | 32650045 | 20318948 | 0.6223 | 2.5715 |
| NC_007175.2 | 17244 | 2385713 | 138.3503 | 156.1746 |
