Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF06-EM02-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF06-EM02-Larvae_1_val_1.fq.gz -2 EF06-EM02-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 00:30:51 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF06-EM02-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 11,759,718 |
| Mapped reads | 11,759,718 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 11,759,718 / 100% |
| Mapped reads, first in pair | 5,879,859 / 50% |
| Mapped reads, second in pair | 5,879,859 / 50% |
| Mapped reads, both in pair | 11,759,718 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 103.21 |
| Overlapping read pairs | 5,838,434 / 99.3% |
| Duplicated reads (estimated) | 3,895,189 / 33.12% |
| Duplication rate | 36.93% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 456,783,875 / 37.68% |
| Number/percentage of C's | 148,693,155 / 12.26% |
| Number/percentage of T's | 459,994,916 / 37.94% |
| Number/percentage of G's | 146,917,523 / 12.12% |
| Number/percentage of N's | 6,984 / 0% |
| GC Percentage | 24.38% |
Coverage
| Mean | 1.7735 |
| Standard Deviation | 4.4935 |
| Mean (paired-end reads overlap ignored) | 0.96 |
Mapping Quality
| Mean Mapping Quality | 16.63 |
Insert size
| Mean | 112.2 |
| Standard Deviation | 50.92 |
| P25/Median/P75 | 76 / 102 / 137 |
Mismatches and indels
| General error rate | 19.32% |
| Mismatches | 233,266,442 |
| Insertions | 893,723 |
| Mapped reads with at least one insertion | 7.29% |
| Deletions | 1,514,115 |
| Mapped reads with at least one deletion | 12.24% |
| Homopolymer indels | 44.84% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 131182020 | 1.9976 | 4.5754 |
| NC_035781.1 | 61752955 | 137514175 | 2.2268 | 5.2446 |
| NC_035782.1 | 77061148 | 159958282 | 2.0757 | 4.9627 |
| NC_035783.1 | 59691872 | 133661989 | 2.2392 | 4.7211 |
| NC_035784.1 | 98698416 | 234700236 | 2.378 | 5.3371 |
| NC_035785.1 | 51258098 | 68217421 | 1.3309 | 3.5649 |
| NC_035786.1 | 57830854 | 79451099 | 1.3739 | 3.4526 |
| NC_035787.1 | 75944018 | 96531730 | 1.2711 | 3.6283 |
| NC_035788.1 | 104168038 | 129485289 | 1.243 | 3.7442 |
| NC_035789.1 | 32650045 | 41624414 | 1.2749 | 3.4479 |
| NC_007175.2 | 17244 | 2093692 | 121.4157 | 86.9161 |
