Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam -nw 400 -hm 3 |
Alignment
| Command line: | "/home/dguevara/pipeline/src/../tools/hisat2-2.1.0/hisat2-align-s --wrapper basic-0 -x ../hcapsulatum/2-alignment/pathogen/indices/hisat2/genome -S ../hcapsulatum/2-alignment/pathogen/sam/genome/SRR949624_hisat2.sam -p 16 -1 ../hcapsulatum/2-alignment/host/fastq/SRR949624_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949624_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Jan 25 04:49:46 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam |
Summary
Globals
| Reference size | 30,483,324 |
| Number of reads | 9,218,978 |
| Mapped reads | 6,036,342 / 65.48% |
| Unmapped reads | 3,182,636 / 34.52% |
| Mapped paired reads | 6,036,342 / 65.48% |
| Mapped reads, first in pair | 3,052,374 / 33.11% |
| Mapped reads, second in pair | 2,983,968 / 32.37% |
| Mapped reads, both in pair | 4,705,357 / 51.04% |
| Mapped reads, singletons | 1,330,985 / 14.44% |
| Read min/max/mean length | 78 / 78 / 78 |
| Duplicated reads (estimated) | 3,164,298 / 34.32% |
| Duplication rate | 36.99% |
| Clipped reads | 951,987 / 10.33% |
ACGT Content
| Number/percentage of A's | 116,286,443 / 24.83% |
| Number/percentage of C's | 118,061,403 / 25.21% |
| Number/percentage of T's | 114,970,528 / 24.55% |
| Number/percentage of G's | 118,962,201 / 25.4% |
| Number/percentage of N's | 203,945,725 / 43.55% |
| GC Percentage | 50.62% |
Coverage
| Mean | 22.0542 |
| Standard Deviation | 78.7599 |
Mapping Quality
| Mean Mapping Quality | 37.71 |
Insert size
| Mean | 2,859.98 |
| Standard Deviation | 31,094.38 |
| P25/Median/P75 | 145 / 189 / 272 |
Mismatches and indels
| General error rate | 0.84% |
| Mismatches | 5,525,396 |
| Insertions | 71,167 |
| Mapped reads with at least one insertion | 1.18% |
| Deletions | 44,627 |
| Mapped reads with at least one deletion | 0.74% |
| Homopolymer indels | 63.64% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| GG663448.1 | 2407 | 53866 | 22.3789 | 31.0487 |
| GG663447.1 | 5093 | 5740 | 1.127 | 1.4996 |
| GG663446.1 | 5267 | 0 | 0 | 0 |
| GG663445.1 | 5726 | 0 | 0 | 0 |
| GG663444.1 | 6104 | 0 | 0 | 0 |
| GG663443.1 | 6704 | 0 | 0 | 0 |
| GG663442.1 | 7013 | 0 | 0 | 0 |
| GG663441.1 | 7428 | 0 | 0 | 0 |
| GG663440.1 | 7433 | 0 | 0 | 0 |
| GG663439.1 | 7612 | 0 | 0 | 0 |
| GG663438.1 | 9352 | 1093 | 0.1169 | 0.5446 |
| GG663437.1 | 9532 | 2618 | 0.2747 | 1.1372 |
| GG663436.1 | 9723 | 158371 | 16.2883 | 18.7998 |
| GG663435.1 | 10315 | 0 | 0 | 0 |
| GG663434.1 | 11106 | 52336 | 4.7124 | 11.5924 |
| GG663433.1 | 11483 | 0 | 0 | 0 |
| GG663432.1 | 11832 | 0 | 0 | 0 |
| GG663431.1 | 11849 | 1468 | 0.1239 | 0.9976 |
| GG663430.1 | 11959 | 0 | 0 | 0 |
| GG663429.1 | 12280 | 152 | 0.0124 | 0.1563 |
| GG663428.1 | 12330 | 803 | 0.0651 | 0.1915 |
| GG663427.1 | 12422 | 467 | 0.0376 | 0.4146 |
| GG663426.1 | 14805 | 0 | 0 | 0 |
| GG663425.1 | 15274 | 9649 | 0.6317 | 0.7355 |
| GG663424.1 | 15855 | 221 | 0.0139 | 0.1523 |
| GG663423.1 | 16334 | 156 | 0.0096 | 0.1248 |
| GG663422.1 | 16757 | 55761 | 3.3276 | 7.1687 |
| GG663421.1 | 17071 | 0 | 0 | 0 |
| GG663420.1 | 17227 | 0 | 0 | 0 |
| GG663419.1 | 17524 | 1437 | 0.082 | 0.6824 |
| GG663418.1 | 17580 | 310 | 0.0176 | 0.2085 |
| GG663417.1 | 18806 | 0 | 0 | 0 |
| GG663416.1 | 20314 | 2484 | 0.1223 | 0.6591 |
| GG663415.1 | 20172 | 18540 | 0.9191 | 0.9156 |
| GG663414.1 | 21124 | 156 | 0.0074 | 0.0856 |
| GG663413.1 | 21814 | 388 | 0.0178 | 0.1935 |
| GG663412.1 | 22664 | 151 | 0.0067 | 0.0814 |
| GG663411.1 | 23942 | 7646 | 0.3194 | 0.321 |
| GG663410.1 | 24438 | 2926 | 0.1197 | 2.0435 |
| GG663409.1 | 30061 | 29122 | 0.9688 | 1.0096 |
| GG663408.1 | 29608 | 529 | 0.0179 | 0.2599 |
| GG663407.1 | 31202 | 248625 | 7.9682 | 13.3573 |
| GG663406.1 | 31468 | 154 | 0.0049 | 0.0808 |
| GG663405.1 | 33416 | 622 | 0.0186 | 0.2587 |
| GG663404.1 | 33436 | 192 | 0.0057 | 0.0878 |
| GG663403.1 | 34148 | 78 | 0.0023 | 0.0477 |
| GG663402.1 | 35232 | 51117 | 1.4509 | 3.2221 |
| GG663401.1 | 36230 | 877470 | 24.2194 | 33.222 |
| GG663400.1 | 40055 | 1776 | 0.0443 | 0.1275 |
| GG663399.1 | 47125 | 559 | 0.0119 | 0.1661 |
| GG663398.1 | 49169 | 2291 | 0.0466 | 0.8038 |
| GG663397.1 | 50304 | 42005 | 0.835 | 0.9521 |
| GG663396.1 | 51171 | 145 | 0.0028 | 0.0532 |
| GG663395.1 | 53466 | 86961 | 1.6265 | 1.6259 |
| GG663394.1 | 53864 | 2616 | 0.0486 | 0.5764 |
| GG663393.1 | 55852 | 140861 | 2.522 | 14.7935 |
| GG663392.1 | 60589 | 22035 | 0.3637 | 0.4317 |
| GG663391.1 | 76172 | 8554 | 0.1123 | 0.1581 |
| GG663390.1 | 87620 | 465 | 0.0053 | 0.084 |
| GG663389.1 | 88906 | 224 | 0.0025 | 0.0501 |
| GG663388.1 | 95026 | 60986 | 0.6418 | 0.7864 |
| GG663387.1 | 113334 | 3766 | 0.0332 | 0.3309 |
| GG663386.1 | 144210 | 1391771 | 9.651 | 9.6284 |
| GG663385.1 | 156336 | 207739 | 1.3288 | 3.0836 |
| GG663384.1 | 204511 | 1870205 | 9.1448 | 20.505 |
| GG663383.1 | 258077 | 7891635 | 30.5786 | 230.465 |
| GG663382.1 | 261570 | 4533199 | 17.3307 | 28.2566 |
| GG663381.1 | 280411 | 3555103 | 12.6782 | 19.9223 |
| GG663380.1 | 351122 | 7505343 | 21.3753 | 37.9759 |
| GG663379.1 | 441739 | 10155686 | 22.9902 | 41.5039 |
| GG663378.1 | 530530 | 14403960 | 27.1501 | 147.5973 |
| GG663377.1 | 695743 | 14744948 | 21.1931 | 44.0674 |
| GG663376.1 | 920403 | 25343498 | 27.5352 | 107.012 |
| GG663375.1 | 915096 | 15185750 | 16.5947 | 23.7077 |
| GG663374.1 | 967551 | 22124640 | 22.8666 | 66.0334 |
| GG663373.1 | 1058542 | 43745976 | 41.3266 | 187.8686 |
| GG663372.1 | 1221551 | 33795470 | 27.666 | 62.9748 |
| GG663371.1 | 1250234 | 21984345 | 17.5842 | 33.8012 |
| GG663370.1 | 1327755 | 30630513 | 23.0694 | 85.4188 |
| GG663369.1 | 1498222 | 31731378 | 21.1794 | 42.1353 |
| GG663368.1 | 1769553 | 28677334 | 16.206 | 28.3306 |
| GG663367.1 | 2225114 | 52148749 | 23.4364 | 51.5237 |
| GG663366.1 | 2702831 | 96745288 | 35.7941 | 151.6104 |
| GG663365.1 | 2818386 | 57104639 | 20.2615 | 37.2455 |
| GG663364.1 | 2928037 | 63796974 | 21.7883 | 44.6427 |
| GG663363.1 | 3777229 | 80952860 | 21.4318 | 50.9785 |
| GG663450.1 | 4245 | 2789 | 0.657 | 2.47 |
| GG663449.1 | 40201 | 96370 | 2.3972 | 8.5339 |
