Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF08-CM04-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF08-CM04-Larvae_1_val_1.fq.gz -2 CF08-CM04-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 00:30:03 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF08-CM04-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 136,022 |
| Mapped reads | 136,022 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 136,022 / 100% |
| Mapped reads, first in pair | 68,011 / 50% |
| Mapped reads, second in pair | 68,011 / 50% |
| Mapped reads, both in pair | 136,022 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 107.11 |
| Overlapping read pairs | 65,231 / 95.91% |
| Duplicated reads (estimated) | 31,830 / 23.4% |
| Duplication rate | 29.84% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 5,630,788 / 38.7% |
| Number/percentage of C's | 1,654,728 / 11.37% |
| Number/percentage of T's | 5,624,202 / 38.66% |
| Number/percentage of G's | 1,639,630 / 11.27% |
| Number/percentage of N's | 151 / 0% |
| GC Percentage | 22.64% |
Coverage
| Mean | 0.0213 |
| Standard Deviation | 0.2203 |
| Mean (paired-end reads overlap ignored) | 0.01 |
Mapping Quality
| Mean Mapping Quality | 18.93 |
Insert size
| Mean | 129.85 |
| Standard Deviation | 76.82 |
| P25/Median/P75 | 76 / 113 / 167 |
Mismatches and indels
| General error rate | 18.94% |
| Mismatches | 2,739,248 |
| Insertions | 12,720 |
| Mapped reads with at least one insertion | 8.77% |
| Deletions | 13,665 |
| Mapped reads with at least one deletion | 9.59% |
| Homopolymer indels | 46.58% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 1580467 | 0.0241 | 0.2158 |
| NC_035781.1 | 61752955 | 1618795 | 0.0262 | 0.2254 |
| NC_035782.1 | 77061148 | 1864886 | 0.0242 | 0.2156 |
| NC_035783.1 | 59691872 | 1580894 | 0.0265 | 0.2251 |
| NC_035784.1 | 98698416 | 2700982 | 0.0274 | 0.2309 |
| NC_035785.1 | 51258098 | 785111 | 0.0153 | 0.1709 |
| NC_035786.1 | 57830854 | 882023 | 0.0153 | 0.1744 |
| NC_035787.1 | 75944018 | 1211694 | 0.016 | 0.1759 |
| NC_035788.1 | 104168038 | 1592802 | 0.0153 | 0.1734 |
| NC_035789.1 | 32650045 | 499011 | 0.0153 | 0.1709 |
| NC_007175.2 | 17244 | 251912 | 14.6087 | 10.1791 |
