Input data and parameters
QualiMap command line
| qualimap bamqc -bam EF08-EM03-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 EF08-EM03-Larvae_1_val_1.fq.gz -2 EF08-EM03-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 06:31:54 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | EF08-EM03-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 17,803,808 |
| Mapped reads | 17,803,808 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 17,803,808 / 100% |
| Mapped reads, first in pair | 8,901,904 / 50% |
| Mapped reads, second in pair | 8,901,904 / 50% |
| Mapped reads, both in pair | 17,803,808 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 101.69 |
| Overlapping read pairs | 8,759,599 / 98.4% |
| Duplicated reads (estimated) | 7,498,881 / 42.12% |
| Duplication rate | 42.6% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 684,457,126 / 37.85% |
| Number/percentage of C's | 219,632,722 / 12.14% |
| Number/percentage of T's | 686,694,019 / 37.97% |
| Number/percentage of G's | 217,765,753 / 12.04% |
| Number/percentage of N's | 9,807 / 0% |
| GC Percentage | 24.18% |
Coverage
| Mean | 2.6445 |
| Standard Deviation | 6.5423 |
| Mean (paired-end reads overlap ignored) | 1.47 |
Mapping Quality
| Mean Mapping Quality | 19.87 |
Insert size
| Mean | 113.92 |
| Standard Deviation | 59.94 |
| P25/Median/P75 | 72 / 100 / 140 |
Mismatches and indels
| General error rate | 19.65% |
| Mismatches | 353,900,887 |
| Insertions | 1,302,945 |
| Mapped reads with at least one insertion | 6.95% |
| Deletions | 1,663,676 |
| Mapped reads with at least one deletion | 8.97% |
| Homopolymer indels | 46.65% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 206778184 | 3.1488 | 7.1028 |
| NC_035781.1 | 61752955 | 211114931 | 3.4187 | 7.8483 |
| NC_035782.1 | 77061148 | 237073495 | 3.0764 | 7.2475 |
| NC_035783.1 | 59691872 | 203123159 | 3.4029 | 7.12 |
| NC_035784.1 | 98698416 | 343749153 | 3.4828 | 7.6934 |
| NC_035785.1 | 51258098 | 94718530 | 1.8479 | 5.152 |
| NC_035786.1 | 57830854 | 110208082 | 1.9057 | 4.9661 |
| NC_035787.1 | 75944018 | 151181946 | 1.9907 | 5.4315 |
| NC_035788.1 | 104168038 | 189272303 | 1.817 | 5.1748 |
| NC_035789.1 | 32650045 | 62194523 | 1.9049 | 5.3922 |
| NC_007175.2 | 17244 | 1392363 | 80.7448 | 52.8717 |
