Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF03-CM04-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF03-CM04-Larvae_1_val_1.fq.gz -2 CF03-CM04-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 00:33:12 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF03-CM04-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 12,497,048 |
| Mapped reads | 12,497,048 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 12,497,048 / 100% |
| Mapped reads, first in pair | 6,248,524 / 50% |
| Mapped reads, second in pair | 6,248,524 / 50% |
| Mapped reads, both in pair | 12,497,048 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 109.18 |
| Overlapping read pairs | 6,057,711 / 96.95% |
| Duplicated reads (estimated) | 4,482,034 / 35.86% |
| Duplication rate | 36.87% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 524,212,645 / 38.47% |
| Number/percentage of C's | 157,660,373 / 11.57% |
| Number/percentage of T's | 524,587,153 / 38.49% |
| Number/percentage of G's | 156,349,667 / 11.47% |
| Number/percentage of N's | 8,412 / 0% |
| GC Percentage | 23.04% |
Coverage
| Mean | 1.993 |
| Standard Deviation | 4.8055 |
| Mean (paired-end reads overlap ignored) | 1.16 |
Mapping Quality
| Mean Mapping Quality | 19.24 |
Insert size
| Mean | 128.58 |
| Standard Deviation | 69.34 |
| P25/Median/P75 | 79 / 112 / 161 |
Mismatches and indels
| General error rate | 19.58% |
| Mismatches | 265,604,614 |
| Insertions | 1,055,405 |
| Mapped reads with at least one insertion | 7.97% |
| Deletions | 1,374,899 |
| Mapped reads with at least one deletion | 10.49% |
| Homopolymer indels | 47.04% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 156703835 | 2.3863 | 5.2402 |
| NC_035781.1 | 61752955 | 156347147 | 2.5318 | 5.6454 |
| NC_035782.1 | 77061148 | 180819035 | 2.3464 | 5.4156 |
| NC_035783.1 | 59691872 | 155287635 | 2.6015 | 5.0851 |
| NC_035784.1 | 98698416 | 259079766 | 2.625 | 5.4488 |
| NC_035785.1 | 51258098 | 72210392 | 1.4088 | 3.7666 |
| NC_035786.1 | 57830854 | 81622464 | 1.4114 | 3.6375 |
| NC_035787.1 | 75944018 | 113182133 | 1.4903 | 3.8312 |
| NC_035788.1 | 104168038 | 140163229 | 1.3455 | 3.7802 |
| NC_035789.1 | 32650045 | 46643719 | 1.4286 | 3.8511 |
| NC_007175.2 | 17244 | 2640936 | 153.151 | 85.2919 |
