Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF04-EM04-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF04-EM04-Zygote_1_val_1.fq.gz -2 EF04-EM04-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 00:30:19 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF04-EM04-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 1,763,276 |
| Mapped reads | 1,763,276 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 1,763,276 / 100% |
| Mapped reads, first in pair | 881,638 / 50% |
| Mapped reads, second in pair | 881,638 / 50% |
| Mapped reads, both in pair | 1,763,276 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 74.31 |
| Overlapping read pairs | 880,645 / 99.89% |
| Duplicated reads (estimated) | 567,383 / 32.18% |
| Duplication rate | 44.19% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 51,760,591 / 39.55% |
| Number/percentage of C's | 13,421,176 / 10.26% |
| Number/percentage of T's | 52,463,682 / 40.09% |
| Number/percentage of G's | 13,223,077 / 10.1% |
| Number/percentage of N's | 859 / 0% |
| GC Percentage | 20.36% |
Coverage
| Mean | 0.1914 |
| Standard Deviation | 0.8262 |
| Mean (paired-end reads overlap ignored) | 0.1 |
Mapping Quality
| Mean Mapping Quality | 12.42 |
Insert size
| Mean | 75.39 |
| Standard Deviation | 28.44 |
| P25/Median/P75 | 56 / 72 / 92 |
Mismatches and indels
| General error rate | 18.33% |
| Mismatches | 23,862,371 |
| Insertions | 108,550 |
| Mapped reads with at least one insertion | 6.06% |
| Deletions | 139,226 |
| Mapped reads with at least one deletion | 7.74% |
| Homopolymer indels | 41.19% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 14737895 | 0.2244 | 0.8165 |
| NC_035781.1 | 61752955 | 15359907 | 0.2487 | 0.8404 |
| NC_035782.1 | 77061148 | 17022653 | 0.2209 | 0.794 |
| NC_035783.1 | 59691872 | 14601169 | 0.2446 | 0.8223 |
| NC_035784.1 | 98698416 | 25296597 | 0.2563 | 0.8483 |
| NC_035785.1 | 51258098 | 7191676 | 0.1403 | 0.6693 |
| NC_035786.1 | 57830854 | 8059151 | 0.1394 | 0.6241 |
| NC_035787.1 | 75944018 | 10370337 | 0.1366 | 0.6062 |
| NC_035788.1 | 104168038 | 13135515 | 0.1261 | 0.5954 |
| NC_035789.1 | 32650045 | 4249419 | 0.1302 | 0.6038 |
| NC_007175.2 | 17244 | 1029542 | 59.7044 | 44.9863 |
