Input data and parameters
QualiMap command line
qualimap bamqc -bam SRR389222_sub3_trimmed_bismark_bt2.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
Command line: | "bismark SRR389222_sub3_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 13:42:16 MSK 2021 |
Size of a homopolymer: | 3 |
Skip duplicate alignments: | no |
Number of windows: | 400 |
BAM file: | SRR389222_sub3_trimmed_bismark_bt2.deduplicated.sorted.bam |
Summary
Globals
Reference size | 48,502 |
Number of reads | 311 |
Mapped reads | 311 / 100% |
Unmapped reads | 0 / 0% |
Mapped paired reads | 0 / 0% |
Secondary alignments | 0 |
Read min/max/mean length | 26 / 36 / 35.25 |
Overlapping read pairs | 0 / 0% |
Duplicated reads (estimated) | 10 / 3.22% |
Duplication rate | 2.99% |
Clipped reads | 0 / 0% |
ACGT Content
Number/percentage of A's | 2,745 / 25.04% |
Number/percentage of C's | 115 / 1.05% |
Number/percentage of T's | 4,831 / 44.07% |
Number/percentage of G's | 3,271 / 29.84% |
Number/percentage of N's | 2 / 0.02% |
GC Percentage | 30.89% |
Coverage
Mean | 0.2261 |
Standard Deviation | 2.7642 |
Mapping Quality
Mean Mapping Quality | 0.38 |
Mismatches and indels
General error rate | 25.81% |
Mismatches | 2,830 |
Chromosome stats
Name | Length | Mapped bases | Mean coverage | Standard deviation |
chr | 48502 | 10964 | 0.2261 | 2.7642 |