Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF05-EM06-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF05-EM06-Larvae_1_val_1.fq.gz -2 EF05-EM06-Larvae_2_val_2.fq.gz --genome BismarkIndex --bam --bowtie2 --multicore 5" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | yes |
| Program: | Bismark (v0.24.2) |
| Analysis date: | Thu Dec 05 11:01:25 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF05-EM06-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 14,255,328 |
| Mapped reads | 14,255,328 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 14,255,328 / 100% |
| Mapped reads, first in pair | 7,127,664 / 50% |
| Mapped reads, second in pair | 7,127,664 / 50% |
| Mapped reads, both in pair | 14,255,328 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 126.34 |
| Overlapping read pairs | 6,592,371 / 92.49% |
| Duplicated reads (estimated) | 4,022,413 / 28.22% |
| Duplication rate | 27.84% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 693,190,989 / 38.54% |
| Number/percentage of C's | 207,059,578 / 11.51% |
| Number/percentage of T's | 692,585,596 / 38.5% |
| Number/percentage of G's | 205,873,392 / 11.45% |
| Number/percentage of N's | 9,565 / 0% |
| GC Percentage | 22.96% |
Coverage
| Mean | 2.631 |
| Standard Deviation | 5.2689 |
| Mean (paired-end reads overlap ignored) | 1.67 |
Mapping Quality
| Mean Mapping Quality | 18.26 |
Insert size
| Mean | 165.32 |
| Standard Deviation | 80.73 |
| P25/Median/P75 | 106 / 149 / 207 |
Mismatches and indels
| General error rate | 17.85% |
| Mismatches | 319,282,452 |
| Insertions | 1,482,620 |
| Mapped reads with at least one insertion | 9.76% |
| Deletions | 2,020,603 |
| Mapped reads with at least one deletion | 13.38% |
| Homopolymer indels | 46.16% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 191242414 | 2.9122 | 5.2655 |
| NC_035781.1 | 61752955 | 193458017 | 3.1328 | 5.7429 |
| NC_035782.1 | 77061148 | 221341982 | 2.8723 | 5.6426 |
| NC_035783.1 | 59691872 | 201923454 | 3.3828 | 5.5254 |
| NC_035784.1 | 98698416 | 369627870 | 3.745 | 6.2785 |
| NC_035785.1 | 51258098 | 98684583 | 1.9252 | 4.7356 |
| NC_035786.1 | 57830854 | 110016886 | 1.9024 | 4.3512 |
| NC_035787.1 | 75944018 | 157791923 | 2.0777 | 4.3621 |
| NC_035788.1 | 104168038 | 191546164 | 1.8388 | 4.3554 |
| NC_035789.1 | 32650045 | 63656864 | 1.9497 | 4.3666 |
| NC_007175.2 | 17244 | 2257106 | 130.8923 | 65.3733 |
