Input data and parameters
QualiMap command line
| qualimap bamqc -bam CF06-CM01-Zygote.deduplicated.sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -1 CF06-CM01-Zygote_1_val_1.fq.gz -2 CF06-CM01-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 00:25:37 GMT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | CF06-CM01-Zygote.deduplicated.sorted.bam |
Summary
Globals
| Reference size | 684,741,128 |
| Number of reads | 9,010,546 |
| Mapped reads | 9,010,546 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 9,010,546 / 100% |
| Mapped reads, first in pair | 4,505,273 / 50% |
| Mapped reads, second in pair | 4,505,273 / 50% |
| Mapped reads, both in pair | 9,010,546 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 20 / 150 / 93.81 |
| Overlapping read pairs | 4,499,196 / 99.87% |
| Duplicated reads (estimated) | 3,014,808 / 33.46% |
| Duplication rate | 39.32% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 330,312,996 / 39.12% |
| Number/percentage of C's | 90,642,137 / 10.74% |
| Number/percentage of T's | 333,968,403 / 39.56% |
| Number/percentage of G's | 89,345,338 / 10.58% |
| Number/percentage of N's | 5,370 / 0% |
| GC Percentage | 21.32% |
Coverage
| Mean | 1.2351 |
| Standard Deviation | 3.3811 |
| Mean (paired-end reads overlap ignored) | 0.64 |
Mapping Quality
| Mean Mapping Quality | 13.79 |
Insert size
| Mean | 97.86 |
| Standard Deviation | 40.79 |
| P25/Median/P75 | 68 / 91 / 120 |
Mismatches and indels
| General error rate | 16.21% |
| Mismatches | 136,108,440 |
| Insertions | 688,690 |
| Mapped reads with at least one insertion | 7.4% |
| Deletions | 1,063,308 |
| Mapped reads with at least one deletion | 11.31% |
| Homopolymer indels | 43.45% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NC_035780.1 | 65668440 | 92384120 | 1.4068 | 3.1749 |
| NC_035781.1 | 61752955 | 96777662 | 1.5672 | 3.5098 |
| NC_035782.1 | 77061148 | 110731306 | 1.4369 | 3.4715 |
| NC_035783.1 | 59691872 | 94037887 | 1.5754 | 3.4142 |
| NC_035784.1 | 98698416 | 161282201 | 1.6341 | 3.5221 |
| NC_035785.1 | 51258098 | 46388676 | 0.905 | 2.684 |
| NC_035786.1 | 57830854 | 52763330 | 0.9124 | 2.4785 |
| NC_035787.1 | 75944018 | 68626448 | 0.9036 | 2.5065 |
| NC_035788.1 | 104168038 | 90423278 | 0.8681 | 2.5767 |
| NC_035789.1 | 32650045 | 28166648 | 0.8627 | 2.507 |
| NC_007175.2 | 17244 | 4140744 | 240.1267 | 153.1249 |
