Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF03-CM05-Larvae.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF03-CM05-Larvae_1_val_1.fq.gz -2 CF03-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: | Wed Dec 04 22:05:33 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF03-CM05-Larvae.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 10,789,144 |
| Mapped reads | 10,789,144 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 10,789,144 / 100% |
| Mapped reads, first in pair | 5,394,572 / 50% |
| Mapped reads, second in pair | 5,394,572 / 50% |
| Mapped reads, both in pair | 10,789,144 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 108.13 |
| Overlapping read pairs | 5,336,229 / 98.92% |
| Duplicated reads (estimated) | 3,376,034 / 31.29% |
| Duplication rate | 34.54% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 438,175,012 / 37.6% |
| Number/percentage of C's | 143,928,265 / 12.35% |
| Number/percentage of T's | 440,858,970 / 37.83% |
| Number/percentage of G's | 142,283,263 / 12.21% |
| Number/percentage of N's | 6,770 / 0% |
| GC Percentage | 24.56% |
Coverage
| Mean | 1.7047 |
| Standard Deviation | 4.6205 |
| Mean (paired-end reads overlap ignored) | 0.94 |
Mapping Quality
| Mean Mapping Quality | 15.09 |
Insert size
| Mean | 119.94 |
| Standard Deviation | 54.58 |
| P25/Median/P75 | 81 / 109 / 147 |
Mismatches and indels
| General error rate | 19.43% |
| Mismatches | 225,468,810 |
| Insertions | 897,983 |
| Mapped reads with at least one insertion | 7.97% |
| Deletions | 1,526,180 |
| Mapped reads with at least one deletion | 13.39% |
| Homopolymer indels | 44.63% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 134034741 | 2.0411 | 4.9546 |
| NC_035781.1 | 61752955 | 133120575 | 2.1557 | 5.4161 |
| NC_035782.1 | 77061148 | 156102237 | 2.0257 | 5.1746 |
| NC_035783.1 | 59691872 | 133981040 | 2.2445 | 4.9494 |
| NC_035784.1 | 98698416 | 222319952 | 2.2525 | 5.4844 |
| NC_035785.1 | 51258098 | 61684153 | 1.2034 | 3.4565 |
| NC_035786.1 | 57830854 | 69306637 | 1.1984 | 3.3295 |
| NC_035787.1 | 75944018 | 95486353 | 1.2573 | 3.7198 |
| NC_035788.1 | 104168038 | 117974947 | 1.1325 | 3.666 |
| NC_035789.1 | 32650045 | 41052568 | 1.2574 | 3.7067 |
| NC_007175.2 | 17244 | 2238800 | 129.8307 | 79.1587 |
