Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF06-EM06-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF06-EM06-Larvae_1_val_1.fq.gz -2 EF06-EM06-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 00:26:49 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF06-EM06-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 2,495,062 |
| Mapped reads | 2,495,062 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 2,495,062 / 100% |
| Mapped reads, first in pair | 1,247,531 / 50% |
| Mapped reads, second in pair | 1,247,531 / 50% |
| Mapped reads, both in pair | 2,495,062 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 105.04 |
| Overlapping read pairs | 1,243,653 / 99.69% |
| Duplicated reads (estimated) | 673,503 / 26.99% |
| Duplication rate | 33.29% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 103,496,948 / 39.54% |
| Number/percentage of C's | 27,204,233 / 10.39% |
| Number/percentage of T's | 104,226,688 / 39.82% |
| Number/percentage of G's | 26,802,742 / 10.24% |
| Number/percentage of N's | 2,178 / 0% |
| GC Percentage | 20.63% |
Coverage
| Mean | 0.383 |
| Standard Deviation | 1.3946 |
| Mean (paired-end reads overlap ignored) | 0.2 |
Mapping Quality
| Mean Mapping Quality | 15.2 |
Insert size
| Mean | 111.86 |
| Standard Deviation | 44.55 |
| P25/Median/P75 | 80 / 105 / 136 |
Mismatches and indels
| General error rate | 16.35% |
| Mismatches | 42,539,082 |
| Insertions | 231,314 |
| Mapped reads with at least one insertion | 8.86% |
| Deletions | 404,162 |
| Mapped reads with at least one deletion | 15.22% |
| Homopolymer indels | 44.5% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 26397116 | 0.402 | 1.1087 |
| NC_035781.1 | 61752955 | 27878491 | 0.4515 | 1.1968 |
| NC_035782.1 | 77061148 | 32518430 | 0.422 | 1.1899 |
| NC_035783.1 | 59691872 | 28767083 | 0.4819 | 1.2074 |
| NC_035784.1 | 98698416 | 54563909 | 0.5528 | 1.3001 |
| NC_035785.1 | 51258098 | 14857818 | 0.2899 | 0.9838 |
| NC_035786.1 | 57830854 | 16606215 | 0.2872 | 0.9342 |
| NC_035787.1 | 75944018 | 21208300 | 0.2793 | 0.9198 |
| NC_035788.1 | 104168038 | 28008798 | 0.2689 | 0.947 |
| NC_035789.1 | 32650045 | 8827589 | 0.2704 | 0.8968 |
| NC_007175.2 | 17244 | 2647796 | 153.5488 | 78.1771 |
