Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF03-CM03-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF03-CM03-Zygote_1_val_1.fq.gz -2 CF03-CM03-Zygote_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 00:25:40 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF03-CM03-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 10,817,182 |
| Mapped reads | 10,817,182 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 10,817,182 / 100% |
| Mapped reads, first in pair | 5,408,591 / 50% |
| Mapped reads, second in pair | 5,408,591 / 50% |
| Mapped reads, both in pair | 10,817,182 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 91.81 |
| Overlapping read pairs | 5,399,246 / 99.83% |
| Duplicated reads (estimated) | 3,941,213 / 36.43% |
| Duplication rate | 41.05% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 388,198,953 / 39.13% |
| Number/percentage of C's | 106,384,306 / 10.72% |
| Number/percentage of T's | 392,342,570 / 39.55% |
| Number/percentage of G's | 105,030,251 / 10.59% |
| Number/percentage of N's | 5,889 / 0% |
| GC Percentage | 21.31% |
Coverage
| Mean | 1.451 |
| Standard Deviation | 3.9357 |
| Mean (paired-end reads overlap ignored) | 0.76 |
Mapping Quality
| Mean Mapping Quality | 16.31 |
Insert size
| Mean | 95.89 |
| Standard Deviation | 41.29 |
| P25/Median/P75 | 66 / 88 / 117 |
Mismatches and indels
| General error rate | 16.16% |
| Mismatches | 159,382,966 |
| Insertions | 801,467 |
| Mapped reads with at least one insertion | 7.14% |
| Deletions | 1,220,414 |
| Mapped reads with at least one deletion | 10.8% |
| Homopolymer indels | 45.38% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 111626253 | 1.6998 | 4.0534 |
| NC_035781.1 | 61752955 | 112183306 | 1.8166 | 4.1646 |
| NC_035782.1 | 77061148 | 129849668 | 1.685 | 4.124 |
| NC_035783.1 | 59691872 | 111193127 | 1.8628 | 4.1048 |
| NC_035784.1 | 98698416 | 188569954 | 1.9106 | 4.2928 |
| NC_035785.1 | 51258098 | 53806382 | 1.0497 | 3.1901 |
| NC_035786.1 | 57830854 | 61144054 | 1.0573 | 2.9821 |
| NC_035787.1 | 75944018 | 82711663 | 1.0891 | 3.2011 |
| NC_035788.1 | 104168038 | 106615640 | 1.0235 | 3.1008 |
| NC_035789.1 | 32650045 | 32309888 | 0.9896 | 2.9692 |
| NC_007175.2 | 17244 | 3571766 | 207.1309 | 150.4827 |
