Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_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/SRR949270_hisat2.sam -p 16 -1 ../hcapsulatum/2-alignment/host/fastq/SRR949270_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949270_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Jan 25 04:50:01 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam |
Summary
Globals
| Reference size | 30,483,324 |
| Number of reads | 10,620,354 |
| Mapped reads | 10,258,051 / 96.59% |
| Unmapped reads | 362,303 / 3.41% |
| Mapped paired reads | 10,258,051 / 96.59% |
| Mapped reads, first in pair | 5,154,638 / 48.54% |
| Mapped reads, second in pair | 5,103,413 / 48.05% |
| Mapped reads, both in pair | 10,034,747 / 94.49% |
| Mapped reads, singletons | 223,304 / 2.1% |
| Read min/max/mean length | 78 / 78 / 78 |
| Duplicated reads (estimated) | 5,596,515 / 52.7% |
| Duplication rate | 38.51% |
| Clipped reads | 702,349 / 6.61% |
ACGT Content
| Number/percentage of A's | 200,551,695 / 25.12% |
| Number/percentage of C's | 198,156,091 / 24.82% |
| Number/percentage of T's | 200,263,552 / 25.08% |
| Number/percentage of G's | 199,555,485 / 24.99% |
| Number/percentage of N's | 275,054,526 / 34.45% |
| GC Percentage | 49.81% |
Coverage
| Mean | 35.2194 |
| Standard Deviation | 104.727 |
Mapping Quality
| Mean Mapping Quality | 41.09 |
Insert size
| Mean | 3,682.33 |
| Standard Deviation | 32,270.44 |
| P25/Median/P75 | 152 / 197 / 283 |
Mismatches and indels
| General error rate | 0.09% |
| Mismatches | 915,854 |
| Insertions | 25,885 |
| Mapped reads with at least one insertion | 0.25% |
| Deletions | 19,638 |
| Mapped reads with at least one deletion | 0.19% |
| Homopolymer indels | 82.48% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| GG663448.1 | 2407 | 79598 | 33.0694 | 33.5274 |
| GG663447.1 | 5093 | 535 | 0.105 | 0.3955 |
| GG663446.1 | 5267 | 1696 | 0.322 | 1.2723 |
| GG663445.1 | 5726 | 3429 | 0.5988 | 2.0379 |
| 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 | 10089 | 1.0788 | 3.8575 |
| GG663437.1 | 9532 | 96522 | 10.1261 | 7.9103 |
| GG663436.1 | 9723 | 848578 | 87.2753 | 99.8291 |
| GG663435.1 | 10315 | 0 | 0 | 0 |
| GG663434.1 | 11106 | 142068 | 12.792 | 25.9643 |
| GG663433.1 | 11483 | 0 | 0 | 0 |
| GG663432.1 | 11832 | 0 | 0 | 0 |
| GG663431.1 | 11849 | 1202 | 0.1014 | 0.5783 |
| GG663430.1 | 11959 | 0 | 0 | 0 |
| GG663429.1 | 12280 | 0 | 0 | 0 |
| GG663428.1 | 12330 | 161309 | 13.0826 | 28.5367 |
| GG663427.1 | 12422 | 2079 | 0.1674 | 0.742 |
| GG663426.1 | 14805 | 156 | 0.0105 | 0.1209 |
| GG663425.1 | 15274 | 3111 | 0.2037 | 1.0604 |
| GG663424.1 | 15855 | 0 | 0 | 0 |
| GG663423.1 | 16334 | 102329 | 6.2648 | 15.3775 |
| GG663422.1 | 16757 | 244451 | 14.588 | 22.0886 |
| GG663421.1 | 17071 | 78 | 0.0046 | 0.0674 |
| GG663420.1 | 17227 | 1363 | 0.0791 | 0.4386 |
| GG663419.1 | 17524 | 24357 | 1.3899 | 4.0203 |
| GG663418.1 | 17580 | 312 | 0.0177 | 0.1801 |
| GG663417.1 | 18806 | 0 | 0 | 0 |
| GG663416.1 | 20314 | 3881 | 0.1911 | 1.0276 |
| GG663415.1 | 20172 | 16089 | 0.7976 | 1.4244 |
| GG663414.1 | 21124 | 892 | 0.0422 | 0.2555 |
| GG663413.1 | 21814 | 23475 | 1.0761 | 3.7645 |
| GG663412.1 | 22664 | 78 | 0.0034 | 0.0586 |
| GG663411.1 | 23942 | 0 | 0 | 0 |
| GG663410.1 | 24438 | 0 | 0 | 0 |
| GG663409.1 | 30061 | 23504 | 0.7819 | 0.7833 |
| GG663408.1 | 29608 | 389 | 0.0131 | 0.1564 |
| GG663407.1 | 31202 | 1193565 | 38.2528 | 52.9439 |
| GG663406.1 | 31468 | 0 | 0 | 0 |
| GG663405.1 | 33416 | 312 | 0.0093 | 0.1085 |
| GG663404.1 | 33436 | 234 | 0.007 | 0.0919 |
| GG663403.1 | 34148 | 3161 | 0.0926 | 0.9733 |
| GG663402.1 | 35232 | 201804 | 5.7279 | 9.5769 |
| GG663401.1 | 36230 | 1203413 | 33.2159 | 41.841 |
| GG663400.1 | 40055 | 0 | 0 | 0 |
| GG663399.1 | 47125 | 2846 | 0.0604 | 0.3674 |
| GG663398.1 | 49169 | 0 | 0 | 0 |
| GG663397.1 | 50304 | 6308 | 0.1254 | 0.5355 |
| GG663396.1 | 51171 | 56372 | 1.1016 | 1.3502 |
| GG663395.1 | 53466 | 77185 | 1.4436 | 3.5405 |
| GG663394.1 | 53864 | 79903 | 1.4834 | 6.9274 |
| GG663393.1 | 55852 | 440407 | 7.8853 | 45.9237 |
| GG663392.1 | 60589 | 7780 | 0.1284 | 0.822 |
| GG663391.1 | 76172 | 4269 | 0.056 | 0.4276 |
| GG663390.1 | 87620 | 20851 | 0.238 | 2.4494 |
| GG663389.1 | 88906 | 389 | 0.0044 | 0.0859 |
| GG663388.1 | 95026 | 64557 | 0.6794 | 0.866 |
| GG663387.1 | 113334 | 294995 | 2.6029 | 13.6369 |
| GG663386.1 | 144210 | 76521 | 0.5306 | 1.1134 |
| GG663385.1 | 156336 | 115052 | 0.7359 | 4.1316 |
| GG663384.1 | 204511 | 4162604 | 20.3539 | 32.3879 |
| GG663383.1 | 258077 | 7185685 | 27.8432 | 64.0212 |
| GG663382.1 | 261570 | 5768864 | 22.0548 | 32.2462 |
| GG663381.1 | 280411 | 5766654 | 20.565 | 27.6839 |
| GG663380.1 | 351122 | 14954643 | 42.591 | 74.6512 |
| GG663379.1 | 441739 | 18170640 | 41.1343 | 109.0542 |
| GG663378.1 | 530530 | 17152458 | 32.3308 | 63.4457 |
| GG663377.1 | 695743 | 21367472 | 30.7117 | 49.1168 |
| GG663376.1 | 920403 | 26006518 | 28.2556 | 54.9224 |
| GG663375.1 | 915096 | 24804080 | 27.1054 | 47.2117 |
| GG663374.1 | 967551 | 26133602 | 27.0101 | 53.1285 |
| GG663373.1 | 1058542 | 64766426 | 61.1846 | 267.4083 |
| GG663372.1 | 1221551 | 51658866 | 42.2896 | 119.8819 |
| GG663371.1 | 1250234 | 33644670 | 26.9107 | 43.0871 |
| GG663370.1 | 1327755 | 54019198 | 40.6846 | 276.4985 |
| GG663369.1 | 1498222 | 62922738 | 41.9983 | 68.2549 |
| GG663368.1 | 1769553 | 50949791 | 28.7925 | 51.902 |
| GG663367.1 | 2225114 | 85888653 | 38.5997 | 104.4097 |
| GG663366.1 | 2702831 | 173075146 | 64.0348 | 81.8285 |
| GG663365.1 | 2818386 | 100944920 | 35.8166 | 105.5856 |
| GG663364.1 | 2928037 | 92245858 | 31.5043 | 51.264 |
| GG663363.1 | 3777229 | 126284843 | 33.4332 | 77.3538 |
| GG663450.1 | 4245 | 5818 | 1.3706 | 4.8386 |
| GG663449.1 | 40201 | 83652 | 2.0808 | 6.7858 |
