Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF07-EM03-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF07-EM03-Larvae_1_val_1.fq.gz -2 EF07-EM03-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 00:32:38 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF07-EM03-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 14,368,048 |
| Mapped reads | 14,368,048 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 14,368,048 / 100% |
| Mapped reads, first in pair | 7,184,024 / 50% |
| Mapped reads, second in pair | 7,184,024 / 50% |
| Mapped reads, both in pair | 14,368,048 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 106.82 |
| Overlapping read pairs | 7,055,741 / 98.21% |
| Duplicated reads (estimated) | 5,085,617 / 35.4% |
| Duplication rate | 36.9% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 588,334,528 / 38.38% |
| Number/percentage of C's | 177,928,619 / 11.61% |
| Number/percentage of T's | 590,601,080 / 38.53% |
| Number/percentage of G's | 176,149,009 / 11.49% |
| Number/percentage of N's | 8,675 / 0% |
| GC Percentage | 23.1% |
Coverage
| Mean | 2.2418 |
| Standard Deviation | 5.174 |
| Mean (paired-end reads overlap ignored) | 1.26 |
Mapping Quality
| Mean Mapping Quality | 19.59 |
Insert size
| Mean | 120.9 |
| Standard Deviation | 60.55 |
| P25/Median/P75 | 78 / 107 / 149 |
Mismatches and indels
| General error rate | 19.27% |
| Mismatches | 294,037,173 |
| Insertions | 1,144,153 |
| Mapped reads with at least one insertion | 7.55% |
| Deletions | 1,471,055 |
| Mapped reads with at least one deletion | 9.8% |
| Homopolymer indels | 46.6% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 173441371 | 2.6412 | 5.5716 |
| NC_035781.1 | 61752955 | 180695478 | 2.9261 | 6.2123 |
| NC_035782.1 | 77061148 | 201946667 | 2.6206 | 5.6782 |
| NC_035783.1 | 59691872 | 174506705 | 2.9235 | 5.7502 |
| NC_035784.1 | 98698416 | 292660380 | 2.9652 | 5.9056 |
| NC_035785.1 | 51258098 | 82269703 | 1.605 | 4.3236 |
| NC_035786.1 | 57830854 | 92712979 | 1.6032 | 4.0063 |
| NC_035787.1 | 75944018 | 126439656 | 1.6649 | 4.2144 |
| NC_035788.1 | 104168038 | 158913411 | 1.5255 | 4.0789 |
| NC_035789.1 | 32650045 | 49640766 | 1.5204 | 4.0218 |
| NC_007175.2 | 17244 | 1796444 | 104.1779 | 60.8174 |
