Input data and parameters
QualiMap command line
| qualimap bamqc -bam LG1-016252-18horse/LC061273_1/sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "/data/shares/horsecov/.snakemake/conda/872b36850c9d6157ac4050b6010d8f56/bin/bowtie2-align-s --wrapper basic-0 -x LC061273_1/LC061273_1 -S LG1-016252-18horse/LC061273_1/mapped.sam -p 32 -1 LG1-016252-18horse/reads_1.fastq -2 LG1-016252-18horse/reads_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | bowtie2 (2.4.4) |
| Analysis date: | Thu Nov 18 14:15:47 EST 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | LG1-016252-18horse/LC061273_1/sorted.bam |
Summary
Globals
| Reference size | 30,916 |
| Number of reads | 298,093,978 |
| Mapped reads | 2,756,177 / 0.92% |
| Unmapped reads | 295,337,801 / 99.08% |
| Mapped paired reads | 2,756,177 / 0.92% |
| Mapped reads, first in pair | 1,379,252 / 0.46% |
| Mapped reads, second in pair | 1,376,925 / 0.46% |
| Mapped reads, both in pair | 2,745,146 / 0.92% |
| Mapped reads, singletons | 11,031 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 15 / 150 / 141.89 |
| Duplicated reads (estimated) | 2,726,724 / 0.91% |
| Duplication rate | 97.73% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 123,839,592 / 30.94% |
| Number/percentage of C's | 76,010,695 / 18.99% |
| Number/percentage of T's | 124,060,972 / 31% |
| Number/percentage of G's | 76,310,072 / 19.07% |
| Number/percentage of N's | 11,086 / 0% |
| GC Percentage | 38.06% |
Coverage
| Mean | 12,954.0089 |
| Standard Deviation | 11,397.5949 |
Mapping Quality
| Mean Mapping Quality | 41.12 |
Insert size
| Mean | 260.12 |
| Standard Deviation | 877.71 |
| P25/Median/P75 | 162 / 211 / 278 |
Mismatches and indels
| General error rate | 0.97% |
| Mismatches | 3,719,949 |
| Insertions | 51,874 |
| Mapped reads with at least one insertion | 1.67% |
| Deletions | 112,411 |
| Mapped reads with at least one deletion | 3.94% |
| Homopolymer indels | 30.32% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| LC061273.1 | 30916 | 400486140 | 12,954.0089 | 11,397.5949 |
