Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF03-EM04-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF03-EM04-Larvae_1_val_1.fq.gz -2 EF03-EM04-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 00:30:51 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF03-EM04-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 11,668,670 |
| Mapped reads | 11,668,670 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 11,668,670 / 100% |
| Mapped reads, first in pair | 5,834,335 / 50% |
| Mapped reads, second in pair | 5,834,335 / 50% |
| Mapped reads, both in pair | 11,668,670 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 100.69 |
| Overlapping read pairs | 5,807,308 / 99.54% |
| Duplicated reads (estimated) | 3,813,911 / 32.69% |
| Duplication rate | 37.28% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 444,505,592 / 37.88% |
| Number/percentage of C's | 141,524,921 / 12.06% |
| Number/percentage of T's | 447,826,932 / 38.16% |
| Number/percentage of G's | 139,643,913 / 11.9% |
| Number/percentage of N's | 7,252 / 0% |
| GC Percentage | 23.96% |
Coverage
| Mean | 1.7171 |
| Standard Deviation | 3.9543 |
| Mean (paired-end reads overlap ignored) | 0.92 |
Mapping Quality
| Mean Mapping Quality | 15.44 |
Insert size
| Mean | 107.88 |
| Standard Deviation | 47.63 |
| P25/Median/P75 | 74 / 99 / 132 |
Mismatches and indels
| General error rate | 18.31% |
| Mismatches | 213,875,986 |
| Insertions | 902,969 |
| Mapped reads with at least one insertion | 7.43% |
| Deletions | 1,707,139 |
| Mapped reads with at least one deletion | 13.79% |
| Homopolymer indels | 43.88% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 131870101 | 2.0081 | 4.5079 |
| NC_035781.1 | 61752955 | 137362552 | 2.2244 | 4.4807 |
| NC_035782.1 | 77061148 | 153816759 | 1.996 | 4.2908 |
| NC_035783.1 | 59691872 | 130682522 | 2.1893 | 4.1373 |
| NC_035784.1 | 98698416 | 226282008 | 2.2927 | 4.6445 |
| NC_035785.1 | 51258098 | 63828080 | 1.2452 | 3.2347 |
| NC_035786.1 | 57830854 | 71720606 | 1.2402 | 3.0465 |
| NC_035787.1 | 75944018 | 96176380 | 1.2664 | 3.1825 |
| NC_035788.1 | 104168038 | 121881483 | 1.17 | 3.0406 |
| NC_035789.1 | 32650045 | 40243710 | 1.2326 | 3.1813 |
| NC_007175.2 | 17244 | 1927948 | 111.804 | 62.6346 |
