Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF08-CM05-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF08-CM05-Larvae_1_val_1.fq.gz -2 CF08-CM05-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 00:30:27 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF08-CM05-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 97,200 |
| Mapped reads | 97,200 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 97,200 / 100% |
| Mapped reads, first in pair | 48,600 / 50% |
| Mapped reads, second in pair | 48,600 / 50% |
| Mapped reads, both in pair | 97,200 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 121.3 |
| Overlapping read pairs | 43,539 / 89.59% |
| Duplicated reads (estimated) | 18,396 / 18.93% |
| Duplication rate | 22.44% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 4,703,030 / 39.95% |
| Number/percentage of C's | 1,209,125 / 10.27% |
| Number/percentage of T's | 4,643,936 / 39.45% |
| Number/percentage of G's | 1,215,246 / 10.32% |
| Number/percentage of N's | 108 / 0% |
| GC Percentage | 20.6% |
Coverage
| Mean | 0.0172 |
| Standard Deviation | 0.1887 |
| Mean (paired-end reads overlap ignored) | 0.01 |
Mapping Quality
| Mean Mapping Quality | 18.17 |
Insert size
| Mean | 166.14 |
| Standard Deviation | 93.73 |
| P25/Median/P75 | 96 / 147 / 214 |
Mismatches and indels
| General error rate | 18.95% |
| Mismatches | 2,214,398 |
| Insertions | 11,770 |
| Mapped reads with at least one insertion | 11.27% |
| Deletions | 11,642 |
| Mapped reads with at least one deletion | 11.38% |
| Homopolymer indels | 47.68% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 1323943 | 0.0202 | 0.1959 |
| NC_035781.1 | 61752955 | 1272053 | 0.0206 | 0.1936 |
| NC_035782.1 | 77061148 | 1451604 | 0.0188 | 0.1863 |
| NC_035783.1 | 59691872 | 1289183 | 0.0216 | 0.2016 |
| NC_035784.1 | 98698416 | 2145869 | 0.0217 | 0.1993 |
| NC_035785.1 | 51258098 | 679859 | 0.0133 | 0.1598 |
| NC_035786.1 | 57830854 | 781630 | 0.0135 | 0.213 |
| NC_035787.1 | 75944018 | 1008148 | 0.0133 | 0.1585 |
| NC_035788.1 | 104168038 | 1302849 | 0.0125 | 0.1539 |
| NC_035789.1 | 32650045 | 484848 | 0.0148 | 0.245 |
| NC_007175.2 | 17244 | 47933 | 2.7797 | 2.5866 |
