Input data and parameters
QualiMap command line
| qualimap bamqc -bam SRR389222_sub1_trimmed_bismark_bt2.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark SRR389222_sub1_trimmed.fq.gz --bowtie2 --bam --genome BismarkIndex" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | yes |
| Program: | Bismark (v0.23.1) |
| Analysis date: | Mon Sep 13 13:42:14 MSK 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | SRR389222_sub1_trimmed_bismark_bt2.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 48,502 |
| Number of reads | 310 |
| Mapped reads | 310 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 36 / 35.14 |
| Overlapping read pairs | 0 / 0% |
| Duplicated reads (estimated) | 9 / 2.9% |
| Duplication rate | 2.99% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 2,735 / 25.11% |
| Number/percentage of C's | 110 / 1.01% |
| Number/percentage of T's | 4,796 / 44.04% |
| Number/percentage of G's | 3,250 / 29.84% |
| Number/percentage of N's | 2 / 0.02% |
| GC Percentage | 30.85% |
Coverage
| Mean | 0.2246 |
| Standard Deviation | 2.7428 |
Mapping Quality
| Mean Mapping Quality | 0.4 |
Mismatches and indels
| General error rate | 25.69% |
| Mismatches | 2,798 |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr | 48502 | 10893 | 0.2246 | 2.7428 |
