Input data and parameters
QualiMap command line
| qualimap bamqc -bam SRR7062655_1.bam -c -nw 400 -hm 3 -sd |
Alignment
| Command line: | bwa mem -K 100000000 -R @RG\tID:1\tPU:1\tSM:SRR7062655\tLB:SRR7062655\tPL:illumina -t 10 -M Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa SRR7062655_R1.fastq.gz SRR7062655_R2.fastq.gz |
| Draw chromosome limits: | yes |
| Analyze overlapping paired-end reads: | no |
| Program: | bwa (0.7.17-r1188) |
| Analysis date: | Mon Oct 25 12:08:07 UTC 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | yes (only flagged) |
| Number of windows: | 400 |
| BAM file: | SRR7062655_1.bam |
Summary
Warnings
| No flagged duplicates are detected | Make sure duplicate alignments are flagged in the BAM file or apply a different skip duplicates mode. |
Globals
| Reference size | 8,220,070 |
| Number of reads | 1,921,198 |
| Mapped reads | 1,919,576 / 99.92% |
| Unmapped reads | 1,622 / 0.08% |
| Mapped paired reads | 1,919,576 / 99.92% |
| Mapped reads, first in pair | 959,862 / 49.96% |
| Mapped reads, second in pair | 959,714 / 49.95% |
| Mapped reads, both in pair | 1,917,954 / 99.83% |
| Mapped reads, singletons | 1,622 / 0.08% |
| Secondary alignments | 721 |
| Read min/max/mean length | 30 / 90 / 90.02 |
| Duplicated reads (flagged) | 0 / 0% |
| Duplicated reads (estimated) | 355,232 / 18.49% |
| Duplication rate | 18.19% |
| Clipped reads | 57,354 / 2.99% |
ACGT Content
| Number/percentage of A's | 42,369,713 / 24.65% |
| Number/percentage of C's | 43,733,442 / 25.44% |
| Number/percentage of T's | 42,341,849 / 24.63% |
| Number/percentage of G's | 43,409,886 / 25.26% |
| Number/percentage of N's | 24,588 / 0.01% |
| GC Percentage | 50.7% |
Coverage
| Mean | 20.9231 |
| Standard Deviation | 11.7618 |
Mapping Quality
| Mean Mapping Quality | 54.64 |
Insert size
| Mean | 624.12 |
| Standard Deviation | 14,551.18 |
| P25/Median/P75 | 469 / 480 / 491 |
Mismatches and indels
| General error rate | 0.99% |
| Mismatches | 1,624,211 |
| Insertions | 33,195 |
| Mapped reads with at least one insertion | 1.69% |
| Deletions | 38,279 |
| Mapped reads with at least one deletion | 1.92% |
| Homopolymer indels | 45.56% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| 25 | 2906300 | 44481713 | 15.3053 | 13.4978 |
| 26 | 5313770 | 127507464 | 23.9957 | 9.3631 |
