Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF07-CM02-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF07-CM02-Zygote_1_val_1.fq.gz -2 CF07-CM02-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 00:29:23 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF07-CM02-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 7,484,924 |
| Mapped reads | 7,484,924 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 7,484,924 / 100% |
| Mapped reads, first in pair | 3,742,462 / 50% |
| Mapped reads, second in pair | 3,742,462 / 50% |
| Mapped reads, both in pair | 7,484,924 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 91.31 |
| Overlapping read pairs | 3,725,071 / 99.54% |
| Duplicated reads (estimated) | 2,517,953 / 33.64% |
| Duplication rate | 39.61% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 267,533,509 / 39.19% |
| Number/percentage of C's | 72,924,104 / 10.68% |
| Number/percentage of T's | 270,105,286 / 39.57% |
| Number/percentage of G's | 72,087,340 / 10.56% |
| Number/percentage of N's | 3,671 / 0% |
| GC Percentage | 21.24% |
Coverage
| Mean | 0.9984 |
| Standard Deviation | 4.3652 |
| Mean (paired-end reads overlap ignored) | 0.53 |
Mapping Quality
| Mean Mapping Quality | 17.93 |
Insert size
| Mean | 96.92 |
| Standard Deviation | 46.37 |
| P25/Median/P75 | 65 / 87 / 118 |
Mismatches and indels
| General error rate | 17.4% |
| Mismatches | 118,142,102 |
| Insertions | 534,967 |
| Mapped reads with at least one insertion | 6.86% |
| Deletions | 762,628 |
| Mapped reads with at least one deletion | 9.77% |
| Homopolymer indels | 45.81% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 75293951 | 1.1466 | 2.4952 |
| NC_035781.1 | 61752955 | 77242585 | 1.2508 | 2.7154 |
| NC_035782.1 | 77061148 | 87407786 | 1.1343 | 2.5727 |
| NC_035783.1 | 59691872 | 75311656 | 1.2617 | 2.6033 |
| NC_035784.1 | 98698416 | 129234991 | 1.3094 | 2.7121 |
| NC_035785.1 | 51258098 | 36120597 | 0.7047 | 2.0557 |
| NC_035786.1 | 57830854 | 41246210 | 0.7132 | 1.9791 |
| NC_035787.1 | 75944018 | 55196009 | 0.7268 | 1.9835 |
| NC_035788.1 | 104168038 | 72660102 | 0.6975 | 1.9783 |
| NC_035789.1 | 32650045 | 22292134 | 0.6828 | 1.9035 |
| NC_007175.2 | 17244 | 11667219 | 676.5959 | 283.0714 |
