Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF05-EM05-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF05-EM05-Zygote_1_val_1.fq.gz -2 EF05-EM05-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 00:30:18 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF05-EM05-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 2,056,578 |
| Mapped reads | 2,056,578 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 2,056,578 / 100% |
| Mapped reads, first in pair | 1,028,289 / 50% |
| Mapped reads, second in pair | 1,028,289 / 50% |
| Mapped reads, both in pair | 2,056,578 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 65.13 |
| Overlapping read pairs | 1,026,620 / 99.84% |
| Duplicated reads (estimated) | 659,021 / 32.04% |
| Duplication rate | 43.64% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 53,759,304 / 40.17% |
| Number/percentage of C's | 12,817,813 / 9.58% |
| Number/percentage of T's | 54,584,108 / 40.79% |
| Number/percentage of G's | 12,653,333 / 9.46% |
| Number/percentage of N's | 947 / 0% |
| GC Percentage | 19.03% |
Coverage
| Mean | 0.1957 |
| Standard Deviation | 0.8406 |
| Mean (paired-end reads overlap ignored) | 0.1 |
Mapping Quality
| Mean Mapping Quality | 17.64 |
Insert size
| Mean | 66.29 |
| Standard Deviation | 26.59 |
| P25/Median/P75 | 48 / 62 / 78 |
Mismatches and indels
| General error rate | 18.03% |
| Mismatches | 24,027,051 |
| Insertions | 94,149 |
| Mapped reads with at least one insertion | 4.51% |
| Deletions | 127,980 |
| Mapped reads with at least one deletion | 6.12% |
| Homopolymer indels | 45.94% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 14957322 | 0.2278 | 0.7841 |
| NC_035781.1 | 61752955 | 15339766 | 0.2484 | 0.8506 |
| NC_035782.1 | 77061148 | 17413111 | 0.226 | 0.8104 |
| NC_035783.1 | 59691872 | 15020064 | 0.2516 | 0.8524 |
| NC_035784.1 | 98698416 | 25792382 | 0.2613 | 0.8603 |
| NC_035785.1 | 51258098 | 7168517 | 0.1399 | 0.6471 |
| NC_035786.1 | 57830854 | 8121009 | 0.1404 | 0.6324 |
| NC_035787.1 | 75944018 | 10685327 | 0.1407 | 0.6155 |
| NC_035788.1 | 104168038 | 14105142 | 0.1354 | 0.6122 |
| NC_035789.1 | 32650045 | 4282837 | 0.1312 | 0.609 |
| NC_007175.2 | 17244 | 1088134 | 63.1022 | 46.419 |
