Input data and parameters
QualiMap command line
| qualimap bamqc -bam B7_input_d_s.bam -gff genome.gtf -nw 400 -hm 3 |
Alignment
| Command line: | "/usr/local/bin/bowtie2-align-s --wrapper basic-0 --non-deterministic -x bowtie2genome -p 8 -U B7_input.fastq.gz" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | bowtie2 (2.3.2) |
| Analysis date: | Fri Aug 10 15:22:49 UTC 2018 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | B7_input_d_s.bam |
GFF region
| Library protocol: | non-strand-specific |
| Outside statistics: | no |
| GFF file: | genome.gtf |
Summary
Globals
| Reference size | 2,725,537,669 |
| Number of reads | 37,299,406 |
| Mapped reads | 36,270,327 / 97.24% |
| Unmapped reads | 1,029,079 / 2.76% |
| Mapped paired reads | 0 / 0% |
| Read min/max/mean length | 35 / 76 / 74.31 |
| Clipped reads | 0 / 0% |
Globals (inside of regions)
| Regions size/percentage of reference | 1,168,286,534 / 42.86% |
| Mapped reads | 17,548,851 / 47.05% |
| Duplicated reads (estimated) | 171,590 / 0.98% |
| Duplication rate | 0.94% |
ACGT Content (inside of regions)
| Number/percentage of A's | 348,628,926 / 26.74% |
| Number/percentage of C's | 302,732,437 / 23.22% |
| Number/percentage of T's | 349,683,835 / 26.83% |
| Number/percentage of G's | 302,492,692 / 23.21% |
| Number/percentage of N's | 108,283 / 0.01% |
| GC Percentage | 46.43% |
Coverage (inside of regions)
| Mean | 1.116 |
| Standard Deviation | 1.3014 |
Mapping Quality (inside of regions)
| Mean Mapping Quality | 38.58 |
Mismatches and indels (inside of regions)
| General error rate | 0.33% |
| Mismatches | 4,163,567 |
| Insertions | 73,561 |
| Mapped reads with at least one insertion | 0.19% |
| Deletions | 75,675 |
| Mapped reads with at least one deletion | 0.2% |
| Homopolymer indels | 47.64% |
Chromosome stats (inside of regions)
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| 1 | 87833224 | 95037407 | 1.082 | 1.1707 |
| 2 | 91729544 | 93358336 | 1.0178 | 1.2334 |
| 3 | 63799692 | 66314949 | 1.0394 | 1.0851 |
| 4 | 70909143 | 76949418 | 1.0852 | 1.1325 |
| 5 | 74314364 | 82289800 | 1.1073 | 1.1376 |
| 6 | 70481271 | 75829971 | 1.0759 | 1.1158 |
| 7 | 72394548 | 82031120 | 1.1331 | 1.1306 |
| 8 | 62305007 | 102337730 | 1.6425 | 1.427 |
| 9 | 65205555 | 75835235 | 1.163 | 2.3746 |
| 10 | 64472795 | 69547736 | 1.0787 | 1.1146 |
| 11 | 63004071 | 76885240 | 1.2203 | 1.3912 |
| 12 | 45140598 | 49479245 | 1.0961 | 1.133 |
| 13 | 44652192 | 49390921 | 1.1061 | 1.1629 |
| 14 | 48751186 | 51870426 | 1.064 | 1.3593 |
| 15 | 40767811 | 66298920 | 1.6263 | 1.3962 |
| 16 | 38505094 | 41833009 | 1.0864 | 1.1224 |
| 17 | 41899931 | 48272493 | 1.1521 | 1.3057 |
| 18 | 33695330 | 36565486 | 1.0852 | 1.1128 |
| 19 | 29501366 | 34525921 | 1.1703 | 1.1592 |
| X | 51516852 | 26473012 | 0.5139 | 0.7871 |
| Y | 7391595 | 2532948 | 0.3427 | 0.7138 |
| MT | 15365 | 105909 | 6.8929 | 4.3635 |
