Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF08-EM04-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF08-EM04-Larvae_1_val_1.fq.gz -2 EF08-EM04-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 00:25:56 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF08-EM04-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 13,350,292 |
| Mapped reads | 13,350,292 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 13,350,292 / 100% |
| Mapped reads, first in pair | 6,675,146 / 50% |
| Mapped reads, second in pair | 6,675,146 / 50% |
| Mapped reads, both in pair | 13,350,292 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 94.37 |
| Overlapping read pairs | 6,651,158 / 99.64% |
| Duplicated reads (estimated) | 4,847,849 / 36.31% |
| Duplication rate | 40.79% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 472,556,927 / 37.54% |
| Number/percentage of C's | 155,468,940 / 12.35% |
| Number/percentage of T's | 476,787,232 / 37.88% |
| Number/percentage of G's | 153,826,303 / 12.22% |
| Number/percentage of N's | 7,863 / 0% |
| GC Percentage | 24.57% |
Coverage
| Mean | 1.8409 |
| Standard Deviation | 4.7035 |
| Mean (paired-end reads overlap ignored) | 0.97 |
Mapping Quality
| Mean Mapping Quality | 17.45 |
Insert size
| Mean | 100.15 |
| Standard Deviation | 46.04 |
| P25/Median/P75 | 68 / 91 / 122 |
Mismatches and indels
| General error rate | 19.27% |
| Mismatches | 241,598,250 |
| Insertions | 877,602 |
| Mapped reads with at least one insertion | 6.33% |
| Deletions | 1,443,244 |
| Mapped reads with at least one deletion | 10.34% |
| Homopolymer indels | 45.14% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 142812184 | 2.1747 | 5.3105 |
| NC_035781.1 | 61752955 | 147696152 | 2.3917 | 5.5091 |
| NC_035782.1 | 77061148 | 163989394 | 2.128 | 5.1273 |
| NC_035783.1 | 59691872 | 140526977 | 2.3542 | 4.9438 |
| NC_035784.1 | 98698416 | 243068215 | 2.4627 | 5.738 |
| NC_035785.1 | 51258098 | 67303289 | 1.313 | 3.6764 |
| NC_035786.1 | 57830854 | 76267216 | 1.3188 | 3.5224 |
| NC_035787.1 | 75944018 | 103247724 | 1.3595 | 3.7492 |
| NC_035788.1 | 104168038 | 129660709 | 1.2447 | 3.5806 |
| NC_035789.1 | 32650045 | 44413024 | 1.3603 | 3.8552 |
| NC_007175.2 | 17244 | 1575312 | 91.3542 | 65.2261 |
