Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF05-CM02-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF05-CM02-Larvae_1_val_1.fq.gz -2 CF05-CM02-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 03:24:04 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF05-CM02-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 19,933,186 |
| Mapped reads | 19,933,186 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 19,933,186 / 100% |
| Mapped reads, first in pair | 9,966,593 / 50% |
| Mapped reads, second in pair | 9,966,593 / 50% |
| Mapped reads, both in pair | 19,933,186 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 104.52 |
| Overlapping read pairs | 9,881,118 / 99.14% |
| Duplicated reads (estimated) | 7,682,227 / 38.54% |
| Duplication rate | 39.87% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 789,007,520 / 37.91% |
| Number/percentage of C's | 250,447,684 / 12.03% |
| Number/percentage of T's | 793,737,965 / 38.14% |
| Number/percentage of G's | 248,057,816 / 11.92% |
| Number/percentage of N's | 11,056 / 0% |
| GC Percentage | 23.95% |
Coverage
| Mean | 3.0433 |
| Standard Deviation | 7.3929 |
| Mean (paired-end reads overlap ignored) | 1.66 |
Mapping Quality
| Mean Mapping Quality | 19.06 |
Insert size
| Mean | 114.41 |
| Standard Deviation | 52.5 |
| P25/Median/P75 | 77 / 104 / 140 |
Mismatches and indels
| General error rate | 19.59% |
| Mismatches | 406,066,835 |
| Insertions | 1,485,954 |
| Mapped reads with at least one insertion | 7.1% |
| Deletions | 1,957,758 |
| Mapped reads with at least one deletion | 9.43% |
| Homopolymer indels | 46.16% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 236177968 | 3.5965 | 8.272 |
| NC_035781.1 | 61752955 | 234394457 | 3.7957 | 8.7469 |
| NC_035782.1 | 77061148 | 264512428 | 3.4325 | 8.3542 |
| NC_035783.1 | 59691872 | 229196485 | 3.8397 | 7.7368 |
| NC_035784.1 | 98698416 | 390946472 | 3.961 | 8.4323 |
| NC_035785.1 | 51258098 | 112984813 | 2.2042 | 5.848 |
| NC_035786.1 | 57830854 | 130471559 | 2.2561 | 5.781 |
| NC_035787.1 | 75944018 | 178533545 | 2.3509 | 6.0816 |
| NC_035788.1 | 104168038 | 231317631 | 2.2206 | 6.1104 |
| NC_035789.1 | 32650045 | 73524740 | 2.2519 | 6.0888 |
| NC_007175.2 | 17244 | 1842249 | 106.8342 | 64.5881 |
