Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF01-CM02-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF01-CM02-Larvae_1_val_1.fq.gz -2 CF01-CM02-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: | CF01-CM02-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 17,062,072 |
| Mapped reads | 17,062,072 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 17,062,072 / 100% |
| Mapped reads, first in pair | 8,531,036 / 50% |
| Mapped reads, second in pair | 8,531,036 / 50% |
| Mapped reads, both in pair | 17,062,072 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 99.38 |
| Overlapping read pairs | 8,504,529 / 99.69% |
| Duplicated reads (estimated) | 6,689,477 / 39.21% |
| Duplication rate | 41.79% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 637,922,220 / 37.66% |
| Number/percentage of C's | 207,801,024 / 12.27% |
| Number/percentage of T's | 642,412,262 / 37.92% |
| Number/percentage of G's | 205,768,420 / 12.15% |
| Number/percentage of N's | 10,576 / 0% |
| GC Percentage | 24.42% |
Coverage
| Mean | 2.4775 |
| Standard Deviation | 6.0417 |
| Mean (paired-end reads overlap ignored) | 1.31 |
Mapping Quality
| Mean Mapping Quality | 18.63 |
Insert size
| Mean | 105.28 |
| Standard Deviation | 44.45 |
| P25/Median/P75 | 74 / 97 / 128 |
Mismatches and indels
| General error rate | 19.29% |
| Mismatches | 325,488,513 |
| Insertions | 1,205,367 |
| Mapped reads with at least one insertion | 6.76% |
| Deletions | 1,932,135 |
| Mapped reads with at least one deletion | 10.83% |
| Homopolymer indels | 45.59% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 193303626 | 2.9436 | 6.7131 |
| NC_035781.1 | 61752955 | 196105445 | 3.1756 | 6.8339 |
| NC_035782.1 | 77061148 | 221999111 | 2.8808 | 6.4916 |
| NC_035783.1 | 59691872 | 190640250 | 3.1937 | 6.3581 |
| NC_035784.1 | 98698416 | 325306387 | 3.296 | 7.1489 |
| NC_035785.1 | 51258098 | 89739682 | 1.7507 | 4.8102 |
| NC_035786.1 | 57830854 | 102143481 | 1.7662 | 4.7036 |
| NC_035787.1 | 75944018 | 140465176 | 1.8496 | 4.8703 |
| NC_035788.1 | 104168038 | 175301244 | 1.6829 | 4.6662 |
| NC_035789.1 | 32650045 | 58082947 | 1.779 | 4.8428 |
| NC_007175.2 | 17244 | 3380744 | 196.0534 | 102.3512 |
