Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF04-CM04-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF04-CM04-Zygote_1_val_1.fq.gz -2 CF04-CM04-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 00:30:51 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF04-CM04-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 10,799,432 |
| Mapped reads | 10,799,432 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 10,799,432 / 100% |
| Mapped reads, first in pair | 5,399,716 / 50% |
| Mapped reads, second in pair | 5,399,716 / 50% |
| Mapped reads, both in pair | 10,799,432 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 98.81 |
| Overlapping read pairs | 5,374,806 / 99.54% |
| Duplicated reads (estimated) | 3,751,641 / 34.74% |
| Duplication rate | 38.36% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 415,940,497 / 39.03% |
| Number/percentage of C's | 116,133,300 / 10.9% |
| Number/percentage of T's | 419,089,148 / 39.32% |
| Number/percentage of G's | 114,597,634 / 10.75% |
| Number/percentage of N's | 5,575 / 0% |
| GC Percentage | 21.65% |
Coverage
| Mean | 1.5592 |
| Standard Deviation | 4.4844 |
| Mean (paired-end reads overlap ignored) | 0.83 |
Mapping Quality
| Mean Mapping Quality | 16.97 |
Insert size
| Mean | 105.87 |
| Standard Deviation | 47.86 |
| P25/Median/P75 | 72 / 96 / 129 |
Mismatches and indels
| General error rate | 17.08% |
| Mismatches | 181,071,433 |
| Insertions | 862,723 |
| Mapped reads with at least one insertion | 7.65% |
| Deletions | 1,426,905 |
| Mapped reads with at least one deletion | 12.53% |
| Homopolymer indels | 45.95% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 116740317 | 1.7777 | 3.6371 |
| NC_035781.1 | 61752955 | 123395123 | 1.9982 | 4.1078 |
| NC_035782.1 | 77061148 | 139330033 | 1.808 | 3.9764 |
| NC_035783.1 | 59691872 | 118768988 | 1.9897 | 3.8741 |
| NC_035784.1 | 98698416 | 205588338 | 2.083 | 4.0248 |
| NC_035785.1 | 51258098 | 56978199 | 1.1116 | 3.02 |
| NC_035786.1 | 57830854 | 64237970 | 1.1108 | 2.8819 |
| NC_035787.1 | 75944018 | 87653139 | 1.1542 | 2.9153 |
| NC_035788.1 | 104168038 | 112574738 | 1.0807 | 2.9919 |
| NC_035789.1 | 32650045 | 33941445 | 1.0396 | 2.8152 |
| NC_007175.2 | 17244 | 8454521 | 490.2877 | 256.4052 |
