Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_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/SRR950093_hisat2.sam -p 16 -1 ../hcapsulatum/2-alignment/host/fastq/SRR950093_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR950093_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Jan 25 04:55:48 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam |
Summary
Globals
| Reference size | 30,483,324 |
| Number of reads | 17,996,144 |
| Mapped reads | 16,998,173 / 94.45% |
| Unmapped reads | 997,971 / 5.55% |
| Mapped paired reads | 16,998,173 / 94.45% |
| Mapped reads, first in pair | 8,447,431 / 46.94% |
| Mapped reads, second in pair | 8,550,742 / 47.51% |
| Mapped reads, both in pair | 16,183,562 / 89.93% |
| Mapped reads, singletons | 814,611 / 4.53% |
| Read min/max/mean length | 80 / 80 / 80 |
| Duplicated reads (estimated) | 11,598,144 / 64.45% |
| Duplication rate | 43.72% |
| Clipped reads | 919,066 / 5.11% |
ACGT Content
| Number/percentage of A's | 345,384,168 / 25.46% |
| Number/percentage of C's | 332,831,633 / 24.53% |
| Number/percentage of T's | 342,976,753 / 25.28% |
| Number/percentage of G's | 335,606,398 / 24.74% |
| Number/percentage of N's | 834,532,961 / 61.51% |
| GC Percentage | 49.27% |
Coverage
| Mean | 71.8878 |
| Standard Deviation | 302.6794 |
Mapping Quality
| Mean Mapping Quality | 38.24 |
Insert size
| Mean | 2,750.05 |
| Standard Deviation | 30,218.21 |
| P25/Median/P75 | 150 / 184 / 241 |
Mismatches and indels
| General error rate | 0.21% |
| Mismatches | 4,405,954 |
| Insertions | 102,316 |
| Mapped reads with at least one insertion | 0.6% |
| Deletions | 38,317 |
| Mapped reads with at least one deletion | 0.22% |
| Homopolymer indels | 84.87% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| GG663448.1 | 2407 | 131512 | 54.6373 | 57.8181 |
| GG663447.1 | 5093 | 80 | 0.0157 | 0.1243 |
| GG663446.1 | 5267 | 560 | 0.1063 | 0.4538 |
| GG663445.1 | 5726 | 2380 | 0.4156 | 1.6469 |
| GG663444.1 | 6104 | 0 | 0 | 0 |
| GG663443.1 | 6704 | 160 | 0.0239 | 0.1526 |
| 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 | 11424 | 1.2216 | 4.667 |
| GG663437.1 | 9532 | 91062 | 9.5533 | 6.7296 |
| GG663436.1 | 9723 | 475356 | 48.8898 | 52.362 |
| GG663435.1 | 10315 | 0 | 0 | 0 |
| GG663434.1 | 11106 | 202473 | 18.231 | 37.7563 |
| GG663433.1 | 11483 | 0 | 0 | 0 |
| GG663432.1 | 11832 | 0 | 0 | 0 |
| GG663431.1 | 11849 | 481 | 0.0406 | 0.1874 |
| GG663430.1 | 11959 | 0 | 0 | 0 |
| GG663429.1 | 12280 | 0 | 0 | 0 |
| GG663428.1 | 12330 | 1271438 | 103.1174 | 232.8685 |
| GG663427.1 | 12422 | 401 | 0.0323 | 0.1934 |
| GG663426.1 | 14805 | 0 | 0 | 0 |
| GG663425.1 | 15274 | 320 | 0.021 | 0.1432 |
| GG663424.1 | 15855 | 160 | 0.0101 | 0.0999 |
| GG663423.1 | 16334 | 148865 | 9.1138 | 22.4798 |
| GG663422.1 | 16757 | 475790 | 28.3935 | 58.9766 |
| GG663421.1 | 17071 | 0 | 0 | 0 |
| GG663420.1 | 17227 | 320 | 0.0186 | 0.1918 |
| GG663419.1 | 17524 | 3938 | 0.2247 | 0.6472 |
| GG663418.1 | 17580 | 160 | 0.0091 | 0.0991 |
| GG663417.1 | 18806 | 0 | 0 | 0 |
| GG663416.1 | 20314 | 308 | 0.0152 | 0.143 |
| GG663415.1 | 20172 | 1353 | 0.0671 | 0.2981 |
| GG663414.1 | 21124 | 0 | 0 | 0 |
| GG663413.1 | 21814 | 14534 | 0.6663 | 1.8015 |
| GG663412.1 | 22664 | 400 | 0.0176 | 0.1708 |
| GG663411.1 | 23942 | 1035 | 0.0432 | 0.2098 |
| GG663410.1 | 24438 | 0 | 0 | 0 |
| GG663409.1 | 30061 | 236 | 0.0079 | 0.0883 |
| GG663408.1 | 29608 | 641 | 0.0216 | 0.1848 |
| GG663407.1 | 31202 | 4464222 | 143.0749 | 223.0927 |
| GG663406.1 | 31468 | 0 | 0 | 0 |
| GG663405.1 | 33416 | 227 | 0.0068 | 0.0765 |
| GG663404.1 | 33436 | 39010 | 1.1667 | 1.1626 |
| GG663403.1 | 34148 | 1196 | 0.035 | 0.3959 |
| GG663402.1 | 35232 | 37114 | 1.0534 | 2.2152 |
| GG663401.1 | 36230 | 2286170 | 63.1016 | 106.445 |
| GG663400.1 | 40055 | 0 | 0 | 0 |
| GG663399.1 | 47125 | 0 | 0 | 0 |
| GG663398.1 | 49169 | 799 | 0.0163 | 0.1486 |
| GG663397.1 | 50304 | 2388 | 0.0475 | 0.3284 |
| GG663396.1 | 51171 | 2545 | 0.0497 | 0.3815 |
| GG663395.1 | 53466 | 3302 | 0.0618 | 0.438 |
| GG663394.1 | 53864 | 216887 | 4.0266 | 14.8517 |
| GG663393.1 | 55852 | 862437 | 15.4415 | 84.5238 |
| GG663392.1 | 60589 | 2272 | 0.0375 | 0.2932 |
| GG663391.1 | 76172 | 160 | 0.0021 | 0.0477 |
| GG663390.1 | 87620 | 5961 | 0.068 | 0.6778 |
| GG663389.1 | 88906 | 640 | 0.0072 | 0.106 |
| GG663388.1 | 95026 | 3815 | 0.0401 | 0.314 |
| GG663387.1 | 113334 | 125527 | 1.1076 | 4.9238 |
| GG663386.1 | 144210 | 15160 | 0.1051 | 0.7686 |
| GG663385.1 | 156336 | 240751 | 1.54 | 12.2298 |
| GG663384.1 | 204511 | 5772029 | 28.2236 | 62.1536 |
| GG663383.1 | 258077 | 18741733 | 72.6207 | 408.0893 |
| GG663382.1 | 261570 | 9201784 | 35.179 | 81.3105 |
| GG663381.1 | 280411 | 10469971 | 37.3379 | 51.3903 |
| GG663380.1 | 351122 | 28309263 | 80.6251 | 173.5212 |
| GG663379.1 | 441739 | 26852162 | 60.7874 | 154.7338 |
| GG663378.1 | 530530 | 26001703 | 49.0108 | 111.1865 |
| GG663377.1 | 695743 | 31427848 | 45.1716 | 116.0255 |
| GG663376.1 | 920403 | 56520944 | 61.4089 | 281.0266 |
| GG663375.1 | 915096 | 43007515 | 46.9978 | 97.011 |
| GG663374.1 | 967551 | 47780003 | 49.3824 | 127.234 |
| GG663373.1 | 1058542 | 220683288 | 208.4785 | 1,164.7895 |
| GG663372.1 | 1221551 | 110515570 | 90.4715 | 251.9224 |
| GG663371.1 | 1250234 | 70873685 | 56.6883 | 188.9351 |
| GG663370.1 | 1327755 | 77238970 | 58.1726 | 143.6662 |
| GG663369.1 | 1498222 | 83817286 | 55.9445 | 181.4466 |
| GG663368.1 | 1769553 | 91667004 | 51.8024 | 128.2882 |
| GG663367.1 | 2225114 | 137776255 | 61.9187 | 207.9378 |
| GG663366.1 | 2702831 | 373493365 | 138.186 | 190.3528 |
| GG663365.1 | 2818386 | 291359512 | 103.3781 | 437.6702 |
| GG663364.1 | 2928037 | 163657072 | 55.8931 | 116.4276 |
| GG663363.1 | 3777229 | 254763629 | 67.4472 | 219.2154 |
| GG663450.1 | 4245 | 14764 | 3.478 | 11.211 |
| GG663449.1 | 40201 | 286906 | 7.1368 | 15.9727 |
