Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF06-CM02-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF06-CM02-Larvae_1_val_1.fq.gz -2 CF06-CM02-Larvae_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 00:30:34 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF06-CM02-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 5,873,698 |
| Mapped reads | 5,873,698 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 5,873,698 / 100% |
| Mapped reads, first in pair | 2,936,849 / 50% |
| Mapped reads, second in pair | 2,936,849 / 50% |
| Mapped reads, both in pair | 5,873,698 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 104.52 |
| Overlapping read pairs | 2,915,310 / 99.27% |
| Duplicated reads (estimated) | 1,635,416 / 27.84% |
| Duplication rate | 33.05% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 233,058,633 / 38.01% |
| Number/percentage of C's | 72,944,587 / 11.9% |
| Number/percentage of T's | 235,273,410 / 38.37% |
| Number/percentage of G's | 71,845,139 / 11.72% |
| Number/percentage of N's | 3,500 / 0% |
| GC Percentage | 23.62% |
Coverage
| Mean | 0.8969 |
| Standard Deviation | 2.4092 |
| Mean (paired-end reads overlap ignored) | 0.49 |
Mapping Quality
| Mean Mapping Quality | 13.75 |
Insert size
| Mean | 114.22 |
| Standard Deviation | 51.84 |
| P25/Median/P75 | 77 / 104 / 141 |
Mismatches and indels
| General error rate | 17.11% |
| Mismatches | 104,318,945 |
| Insertions | 508,807 |
| Mapped reads with at least one insertion | 8.34% |
| Deletions | 734,218 |
| Mapped reads with at least one deletion | 11.93% |
| Homopolymer indels | 42.75% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 67915266 | 1.0342 | 2.4673 |
| NC_035781.1 | 61752955 | 69542081 | 1.1261 | 2.7199 |
| NC_035782.1 | 77061148 | 80079383 | 1.0392 | 2.6028 |
| NC_035783.1 | 59691872 | 69081504 | 1.1573 | 2.7931 |
| NC_035784.1 | 98698416 | 116392594 | 1.1793 | 2.6926 |
| NC_035785.1 | 51258098 | 32595637 | 0.6359 | 2.0102 |
| NC_035786.1 | 57830854 | 38435173 | 0.6646 | 2.154 |
| NC_035787.1 | 75944018 | 50442077 | 0.6642 | 1.9133 |
| NC_035788.1 | 104168038 | 67051026 | 0.6437 | 2.0098 |
| NC_035789.1 | 32650045 | 21707776 | 0.6649 | 1.9468 |
| NC_007175.2 | 17244 | 907076 | 52.6024 | 44.1618 |
