Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF05-EM01-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF05-EM01-Larvae_1_val_1.fq.gz -2 EF05-EM01-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 00:30:43 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF05-EM01-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 8,495,260 |
| Mapped reads | 8,495,260 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 8,495,260 / 100% |
| Mapped reads, first in pair | 4,247,630 / 50% |
| Mapped reads, second in pair | 4,247,630 / 50% |
| Mapped reads, both in pair | 8,495,260 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 109.75 |
| Overlapping read pairs | 4,201,373 / 98.91% |
| Duplicated reads (estimated) | 2,774,639 / 32.66% |
| Duplication rate | 37.21% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 350,270,349 / 37.62% |
| Number/percentage of C's | 115,312,274 / 12.38% |
| Number/percentage of T's | 351,313,896 / 37.73% |
| Number/percentage of G's | 114,281,740 / 12.27% |
| Number/percentage of N's | 5,129 / 0% |
| GC Percentage | 24.66% |
Coverage
| Mean | 1.3619 |
| Standard Deviation | 3.8018 |
| Mean (paired-end reads overlap ignored) | 0.75 |
Mapping Quality
| Mean Mapping Quality | 16.26 |
Insert size
| Mean | 122.16 |
| Standard Deviation | 55.02 |
| P25/Median/P75 | 83 / 111 / 151 |
Mismatches and indels
| General error rate | 19.48% |
| Mismatches | 180,429,668 |
| Insertions | 769,294 |
| Mapped reads with at least one insertion | 8.66% |
| Deletions | 1,012,312 |
| Mapped reads with at least one deletion | 11.38% |
| Homopolymer indels | 44.16% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 105580198 | 1.6078 | 3.8494 |
| NC_035781.1 | 61752955 | 107567017 | 1.7419 | 4.0596 |
| NC_035782.1 | 77061148 | 121456105 | 1.5761 | 3.8917 |
| NC_035783.1 | 59691872 | 105260994 | 1.7634 | 3.8448 |
| NC_035784.1 | 98698416 | 177858192 | 1.802 | 4.8243 |
| NC_035785.1 | 51258098 | 49063759 | 0.9572 | 2.8022 |
| NC_035786.1 | 57830854 | 56611069 | 0.9789 | 2.8015 |
| NC_035787.1 | 75944018 | 76313408 | 1.0049 | 2.9114 |
| NC_035788.1 | 104168038 | 95996620 | 0.9216 | 2.7982 |
| NC_035789.1 | 32650045 | 33497397 | 1.026 | 3.0066 |
| NC_007175.2 | 17244 | 3372128 | 195.5537 | 109.0013 |
