Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_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/SRR949916_hisat2.sam -p 16 -1 ../hcapsulatum/2-alignment/host/fastq/SRR949916_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949916_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Jan 25 04:55:44 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam |
Summary
Globals
| Reference size | 30,483,324 |
| Number of reads | 16,489,196 |
| Mapped reads | 15,585,452 / 94.52% |
| Unmapped reads | 903,744 / 5.48% |
| Mapped paired reads | 15,585,452 / 94.52% |
| Mapped reads, first in pair | 7,739,837 / 46.94% |
| Mapped reads, second in pair | 7,845,615 / 47.58% |
| Mapped reads, both in pair | 14,864,764 / 90.15% |
| Mapped reads, singletons | 720,688 / 4.37% |
| Read min/max/mean length | 80 / 80 / 80 |
| Duplicated reads (estimated) | 10,239,033 / 62.1% |
| Duplication rate | 42.65% |
| Clipped reads | 833,852 / 5.06% |
ACGT Content
| Number/percentage of A's | 319,449,327 / 25.68% |
| Number/percentage of C's | 303,652,491 / 24.41% |
| Number/percentage of T's | 317,021,195 / 25.48% |
| Number/percentage of G's | 303,952,670 / 24.43% |
| Number/percentage of N's | 1,788,396,958 / 143.75% |
| GC Percentage | 48.84% |
Coverage
| Mean | 99.4812 |
| Standard Deviation | 293.7997 |
Mapping Quality
| Mean Mapping Quality | 38.71 |
Insert size
| Mean | 2,332.68 |
| Standard Deviation | 27,472.18 |
| P25/Median/P75 | 148 / 181 / 237 |
Mismatches and indels
| General error rate | 0.14% |
| Mismatches | 3,986,740 |
| Insertions | 110,756 |
| Mapped reads with at least one insertion | 0.71% |
| Deletions | 37,011 |
| Mapped reads with at least one deletion | 0.23% |
| Homopolymer indels | 86.9% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| GG663448.1 | 2407 | 153100 | 63.6061 | 64.322 |
| GG663447.1 | 5093 | 80 | 0.0157 | 0.1243 |
| GG663446.1 | 5267 | 319 | 0.0606 | 0.2948 |
| GG663445.1 | 5726 | 877 | 0.1532 | 0.6555 |
| 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 | 160 | 0.021 | 0.1434 |
| GG663438.1 | 9352 | 17080 | 1.8263 | 6.2577 |
| GG663437.1 | 9532 | 77152 | 8.094 | 6.5687 |
| GG663436.1 | 9723 | 336561 | 34.6149 | 41.3729 |
| GG663435.1 | 10315 | 0 | 0 | 0 |
| GG663434.1 | 11106 | 247527 | 22.2877 | 47.777 |
| GG663433.1 | 11483 | 160 | 0.0139 | 0.1223 |
| GG663432.1 | 11832 | 0 | 0 | 0 |
| GG663431.1 | 11849 | 557 | 0.047 | 0.21 |
| GG663430.1 | 11959 | 320 | 0.0268 | 0.2298 |
| GG663429.1 | 12280 | 0 | 0 | 0 |
| GG663428.1 | 12330 | 828995 | 67.234 | 156.5409 |
| GG663427.1 | 12422 | 1997 | 0.1608 | 0.8825 |
| GG663426.1 | 14805 | 0 | 0 | 0 |
| GG663425.1 | 15274 | 531 | 0.0348 | 0.1858 |
| GG663424.1 | 15855 | 160 | 0.0101 | 0.0999 |
| GG663423.1 | 16334 | 170122 | 10.4152 | 25.1321 |
| GG663422.1 | 16757 | 212211 | 12.664 | 18.7437 |
| GG663421.1 | 17071 | 0 | 0 | 0 |
| GG663420.1 | 17227 | 316 | 0.0183 | 0.1466 |
| GG663419.1 | 17524 | 4152 | 0.2369 | 1.0833 |
| GG663418.1 | 17580 | 227 | 0.0129 | 0.1188 |
| GG663417.1 | 18806 | 0 | 0 | 0 |
| GG663416.1 | 20314 | 1315 | 0.0647 | 0.2812 |
| GG663415.1 | 20172 | 3175 | 0.1574 | 0.726 |
| GG663414.1 | 21124 | 80 | 0.0038 | 0.0614 |
| GG663413.1 | 21814 | 16831 | 0.7716 | 2.5636 |
| GG663412.1 | 22664 | 637 | 0.0281 | 0.1841 |
| GG663411.1 | 23942 | 1200 | 0.0501 | 0.2737 |
| GG663410.1 | 24438 | 0 | 0 | 0 |
| GG663409.1 | 30061 | 80 | 0.0027 | 0.0515 |
| GG663408.1 | 29608 | 1564 | 0.0528 | 0.2769 |
| GG663407.1 | 31202 | 3828975 | 122.7157 | 186.9088 |
| GG663406.1 | 31468 | 0 | 0 | 0 |
| GG663405.1 | 33416 | 160 | 0.0048 | 0.0853 |
| GG663404.1 | 33436 | 640 | 0.0191 | 0.1853 |
| GG663403.1 | 34148 | 2027 | 0.0594 | 0.4442 |
| GG663402.1 | 35232 | 36550 | 1.0374 | 2.1092 |
| GG663401.1 | 36230 | 1917630 | 52.9293 | 80.2463 |
| GG663400.1 | 40055 | 160 | 0.004 | 0.0654 |
| GG663399.1 | 47125 | 80 | 0.0017 | 0.0412 |
| GG663398.1 | 49169 | 640 | 0.013 | 0.1468 |
| GG663397.1 | 50304 | 3346 | 0.0665 | 0.3546 |
| GG663396.1 | 51171 | 4140 | 0.0809 | 0.5124 |
| GG663395.1 | 53466 | 64944 | 1.2147 | 1.2439 |
| GG663394.1 | 53864 | 207762 | 3.8572 | 14.2841 |
| GG663393.1 | 55852 | 759839 | 13.6045 | 73.4447 |
| GG663392.1 | 60589 | 45719 | 0.7546 | 0.8536 |
| GG663391.1 | 76172 | 0 | 0 | 0 |
| GG663390.1 | 87620 | 10478 | 0.1196 | 1.2843 |
| GG663389.1 | 88906 | 717 | 0.0081 | 0.0939 |
| GG663388.1 | 95026 | 5257 | 0.0553 | 0.3933 |
| GG663387.1 | 113334 | 182374 | 1.6092 | 6.8218 |
| GG663386.1 | 144210 | 75630 | 0.5244 | 1.2116 |
| GG663385.1 | 156336 | 328792 | 2.1031 | 16.8885 |
| GG663384.1 | 204511 | 6047999 | 29.573 | 65.5442 |
| GG663383.1 | 258077 | 14921125 | 57.8166 | 192.725 |
| GG663382.1 | 261570 | 8371134 | 32.0034 | 75.0873 |
| GG663381.1 | 280411 | 11099599 | 39.5833 | 64.6964 |
| GG663380.1 | 351122 | 24955044 | 71.0723 | 144.0759 |
| GG663379.1 | 441739 | 23592441 | 53.4081 | 130.6637 |
| GG663378.1 | 530530 | 23531792 | 44.3553 | 109.1913 |
| GG663377.1 | 695743 | 28121728 | 40.4197 | 96.4683 |
| GG663376.1 | 920403 | 53839286 | 58.4953 | 267.3762 |
| GG663375.1 | 915096 | 36977604 | 40.4084 | 80.181 |
| GG663374.1 | 967551 | 55462420 | 57.3225 | 125.2411 |
| GG663373.1 | 1058542 | 1035991264 | 978.6964 | 1,388.1853 |
| GG663372.1 | 1221551 | 82237045 | 67.3218 | 194.337 |
| GG663371.1 | 1250234 | 65549705 | 52.4299 | 172.7962 |
| GG663370.1 | 1327755 | 73285133 | 55.1948 | 135.4455 |
| GG663369.1 | 1498222 | 74795413 | 49.9228 | 163.2358 |
| GG663368.1 | 1769553 | 84859593 | 47.9554 | 112.9326 |
| GG663367.1 | 2225114 | 135261964 | 60.7888 | 214.9358 |
| GG663366.1 | 2702831 | 368885127 | 136.481 | 186.4493 |
| GG663365.1 | 2818386 | 337521772 | 119.7571 | 489.829 |
| GG663364.1 | 2928037 | 140914094 | 48.1258 | 97.5965 |
| GG663363.1 | 3777229 | 336608149 | 89.1151 | 235.7 |
| GG663450.1 | 4245 | 16552 | 3.8992 | 12.3786 |
| GG663449.1 | 40201 | 117942 | 2.9338 | 7.2586 |
