Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF03-EM05-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF03-EM05-Larvae_1_val_1.fq.gz -2 EF03-EM05-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 00:30:57 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF03-EM05-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 10,362,584 |
| Mapped reads | 10,362,584 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 10,362,584 / 100% |
| Mapped reads, first in pair | 5,181,292 / 50% |
| Mapped reads, second in pair | 5,181,292 / 50% |
| Mapped reads, both in pair | 10,362,584 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 106.06 |
| Overlapping read pairs | 5,124,658 / 98.91% |
| Duplicated reads (estimated) | 3,079,780 / 29.72% |
| Duplication rate | 33.63% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 416,813,801 / 37.97% |
| Number/percentage of C's | 131,431,594 / 11.97% |
| Number/percentage of T's | 419,748,650 / 38.24% |
| Number/percentage of G's | 129,766,128 / 11.82% |
| Number/percentage of N's | 6,126 / 0% |
| GC Percentage | 23.79% |
Coverage
| Mean | 1.6058 |
| Standard Deviation | 3.8241 |
| Mean (paired-end reads overlap ignored) | 0.89 |
Mapping Quality
| Mean Mapping Quality | 14.85 |
Insert size
| Mean | 117.69 |
| Standard Deviation | 55.32 |
| P25/Median/P75 | 78 / 106 / 145 |
Mismatches and indels
| General error rate | 18.7% |
| Mismatches | 204,303,648 |
| Insertions | 870,180 |
| Mapped reads with at least one insertion | 8.06% |
| Deletions | 1,313,715 |
| Mapped reads with at least one deletion | 12.07% |
| Homopolymer indels | 43.7% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 122132087 | 1.8598 | 3.9632 |
| NC_035781.1 | 61752955 | 127110859 | 2.0584 | 4.5212 |
| NC_035782.1 | 77061148 | 143936848 | 1.8678 | 4.2583 |
| NC_035783.1 | 59691872 | 123443905 | 2.068 | 4.1127 |
| NC_035784.1 | 98698416 | 209984223 | 2.1275 | 4.3415 |
| NC_035785.1 | 51258098 | 58910000 | 1.1493 | 3.0985 |
| NC_035786.1 | 57830854 | 67106839 | 1.1604 | 3.0253 |
| NC_035787.1 | 75944018 | 90428959 | 1.1907 | 3.106 |
| NC_035788.1 | 104168038 | 118025099 | 1.133 | 3.1457 |
| NC_035789.1 | 32650045 | 36775633 | 1.1264 | 3.0755 |
| NC_007175.2 | 17244 | 1698339 | 98.4887 | 63.5893 |
