Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF04-EM05-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF04-EM05-Larvae_1_val_1.fq.gz -2 EF04-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 00:33:14 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF04-EM05-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 16,787,080 |
| Mapped reads | 16,787,080 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 16,787,080 / 100% |
| Mapped reads, first in pair | 8,393,540 / 50% |
| Mapped reads, second in pair | 8,393,540 / 50% |
| Mapped reads, both in pair | 16,787,080 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 110.53 |
| Overlapping read pairs | 8,241,199 / 98.19% |
| Duplicated reads (estimated) | 6,006,426 / 35.78% |
| Duplication rate | 36.43% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 706,414,715 / 38.11% |
| Number/percentage of C's | 220,089,896 / 11.87% |
| Number/percentage of T's | 708,788,717 / 38.24% |
| Number/percentage of G's | 218,144,800 / 11.77% |
| Number/percentage of N's | 9,840 / 0% |
| GC Percentage | 23.64% |
Coverage
| Mean | 2.7105 |
| Standard Deviation | 6.598 |
| Mean (paired-end reads overlap ignored) | 1.53 |
Mapping Quality
| Mean Mapping Quality | 18.96 |
Insert size
| Mean | 125.54 |
| Standard Deviation | 59.84 |
| P25/Median/P75 | 83 / 112 / 154 |
Mismatches and indels
| General error rate | 19.62% |
| Mismatches | 362,125,841 |
| Insertions | 1,373,557 |
| Mapped reads with at least one insertion | 7.75% |
| Deletions | 1,857,044 |
| Mapped reads with at least one deletion | 10.58% |
| Homopolymer indels | 46.27% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 210643108 | 3.2077 | 7.3335 |
| NC_035781.1 | 61752955 | 215768079 | 3.4941 | 7.7895 |
| NC_035782.1 | 77061148 | 242074161 | 3.1413 | 7.1904 |
| NC_035783.1 | 59691872 | 207796321 | 3.4811 | 7.2621 |
| NC_035784.1 | 98698416 | 350482138 | 3.551 | 7.6779 |
| NC_035785.1 | 51258098 | 99952979 | 1.95 | 5.2793 |
| NC_035786.1 | 57830854 | 112736048 | 1.9494 | 4.9083 |
| NC_035787.1 | 75944018 | 154241709 | 2.031 | 5.382 |
| NC_035788.1 | 104168038 | 193911131 | 1.8615 | 5.0904 |
| NC_035789.1 | 32650045 | 65774597 | 2.0145 | 5.5484 |
| NC_007175.2 | 17244 | 2593343 | 150.391 | 82.5696 |
