Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_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/SRR949060_hisat2.sam -p 16 -1 ../hcapsulatum/2-alignment/host/fastq/SRR949060_1.fastq -2 ../hcapsulatum/2-alignment/host/fastq/SRR949060_2.fastq" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | hisat2 (2.1.0) |
| Analysis date: | Thu Jan 25 04:49:57 CST 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam |
Summary
Globals
| Reference size | 30,483,324 |
| Number of reads | 9,576,101 |
| Mapped reads | 9,226,209 / 96.35% |
| Unmapped reads | 349,892 / 3.65% |
| Mapped paired reads | 9,226,209 / 96.35% |
| Mapped reads, first in pair | 4,633,216 / 48.38% |
| Mapped reads, second in pair | 4,592,993 / 47.96% |
| Mapped reads, both in pair | 8,987,885 / 93.86% |
| Mapped reads, singletons | 238,324 / 2.49% |
| Read min/max/mean length | 78 / 78 / 78 |
| Duplicated reads (estimated) | 4,837,797 / 50.52% |
| Duplication rate | 36.98% |
| Clipped reads | 586,970 / 6.13% |
ACGT Content
| Number/percentage of A's | 181,426,059 / 25.26% |
| Number/percentage of C's | 177,218,602 / 24.68% |
| Number/percentage of T's | 181,033,991 / 25.21% |
| Number/percentage of G's | 178,511,114 / 24.86% |
| Number/percentage of N's | 251,744,425 / 35.05% |
| GC Percentage | 49.53% |
Coverage
| Mean | 31.8193 |
| Standard Deviation | 88.5775 |
Mapping Quality
| Mean Mapping Quality | 40.55 |
Insert size
| Mean | 2,945.61 |
| Standard Deviation | 32,376.04 |
| P25/Median/P75 | 150 / 187 / 253 |
Mismatches and indels
| General error rate | 0.08% |
| Mismatches | 789,163 |
| Insertions | 26,950 |
| Mapped reads with at least one insertion | 0.29% |
| Deletions | 18,383 |
| Mapped reads with at least one deletion | 0.2% |
| Homopolymer indels | 82.67% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| GG663448.1 | 2407 | 61845 | 25.6938 | 29.8561 |
| GG663447.1 | 5093 | 1247 | 0.2448 | 0.8667 |
| GG663446.1 | 5267 | 2255 | 0.4281 | 1.7031 |
| GG663445.1 | 5726 | 3108 | 0.5428 | 2.0456 |
| 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 | 11315 | 1.2099 | 4.5705 |
| GG663437.1 | 9532 | 87070 | 9.1345 | 8.1075 |
| GG663436.1 | 9723 | 846317 | 87.0428 | 101.3377 |
| GG663435.1 | 10315 | 0 | 0 | 0 |
| GG663434.1 | 11106 | 123829 | 11.1497 | 23.2821 |
| GG663433.1 | 11483 | 0 | 0 | 0 |
| GG663432.1 | 11832 | 0 | 0 | 0 |
| GG663431.1 | 11849 | 1209 | 0.102 | 0.6143 |
| GG663430.1 | 11959 | 0 | 0 | 0 |
| GG663429.1 | 12280 | 0 | 0 | 0 |
| GG663428.1 | 12330 | 162698 | 13.1953 | 29.6298 |
| GG663427.1 | 12422 | 1351 | 0.1088 | 0.4606 |
| GG663426.1 | 14805 | 0 | 0 | 0 |
| GG663425.1 | 15274 | 3095 | 0.2026 | 0.9117 |
| GG663424.1 | 15855 | 0 | 0 | 0 |
| GG663423.1 | 16334 | 95588 | 5.8521 | 15.1633 |
| GG663422.1 | 16757 | 221674 | 13.2287 | 19.239 |
| GG663421.1 | 17071 | 0 | 0 | 0 |
| GG663420.1 | 17227 | 1155 | 0.067 | 0.3962 |
| GG663419.1 | 17524 | 13763 | 0.7854 | 2.7273 |
| GG663418.1 | 17580 | 156 | 0.0089 | 0.0938 |
| GG663417.1 | 18806 | 0 | 0 | 0 |
| GG663416.1 | 20314 | 3336 | 0.1642 | 1.2899 |
| GG663415.1 | 20172 | 6244 | 0.3095 | 1.0738 |
| GG663414.1 | 21124 | 312 | 0.0148 | 0.1206 |
| GG663413.1 | 21814 | 27053 | 1.2402 | 4.1942 |
| GG663412.1 | 22664 | 156 | 0.0069 | 0.0827 |
| GG663411.1 | 23942 | 0 | 0 | 0 |
| GG663410.1 | 24438 | 0 | 0 | 0 |
| GG663409.1 | 30061 | 78 | 0.0026 | 0.0509 |
| GG663408.1 | 29608 | 0 | 0 | 0 |
| GG663407.1 | 31202 | 1039744 | 33.323 | 43.4792 |
| GG663406.1 | 31468 | 0 | 0 | 0 |
| GG663405.1 | 33416 | 0 | 0 | 0 |
| GG663404.1 | 33436 | 0 | 0 | 0 |
| GG663403.1 | 34148 | 1295 | 0.0379 | 0.459 |
| GG663402.1 | 35232 | 182346 | 5.1756 | 9.4267 |
| GG663401.1 | 36230 | 1130078 | 31.1918 | 39.3885 |
| GG663400.1 | 40055 | 0 | 0 | 0 |
| GG663399.1 | 47125 | 1246 | 0.0264 | 0.2016 |
| GG663398.1 | 49169 | 156 | 0.0032 | 0.0562 |
| GG663397.1 | 50304 | 7633 | 0.1517 | 0.7888 |
| GG663396.1 | 51171 | 35242 | 0.6887 | 1.1143 |
| GG663395.1 | 53466 | 49168 | 0.9196 | 2.0069 |
| GG663394.1 | 53864 | 76303 | 1.4166 | 6.5447 |
| GG663393.1 | 55852 | 335158 | 6.0008 | 34.1099 |
| GG663392.1 | 60589 | 35140 | 0.58 | 0.8071 |
| GG663391.1 | 76172 | 2649 | 0.0348 | 0.3371 |
| GG663390.1 | 87620 | 19748 | 0.2254 | 2.1354 |
| GG663389.1 | 88906 | 0 | 0 | 0 |
| GG663388.1 | 95026 | 27441 | 0.2888 | 0.7839 |
| GG663387.1 | 113334 | 305605 | 2.6965 | 12.9862 |
| GG663386.1 | 144210 | 32941 | 0.2284 | 1.1067 |
| GG663385.1 | 156336 | 92400 | 0.591 | 3.5245 |
| GG663384.1 | 204511 | 3525412 | 17.2383 | 27.8009 |
| GG663383.1 | 258077 | 6713455 | 26.0134 | 60.3798 |
| GG663382.1 | 261570 | 5167583 | 19.756 | 28.5151 |
| GG663381.1 | 280411 | 5246626 | 18.7105 | 26.3505 |
| GG663380.1 | 351122 | 14022722 | 39.9369 | 69.3984 |
| GG663379.1 | 441739 | 16487105 | 37.3232 | 101.8509 |
| GG663378.1 | 530530 | 16089361 | 30.327 | 57.2145 |
| GG663377.1 | 695743 | 19127644 | 27.4924 | 43.1252 |
| GG663376.1 | 920403 | 24338078 | 26.4428 | 53.3863 |
| GG663375.1 | 915096 | 22681932 | 24.7864 | 44.0252 |
| GG663374.1 | 967551 | 23859972 | 24.6602 | 44.4257 |
| GG663373.1 | 1058542 | 57867280 | 54.667 | 225.6693 |
| GG663372.1 | 1221551 | 47571108 | 38.9432 | 107.741 |
| GG663371.1 | 1250234 | 30690217 | 24.5476 | 39.9936 |
| GG663370.1 | 1327755 | 46141021 | 34.7512 | 211.4943 |
| GG663369.1 | 1498222 | 43997082 | 29.3662 | 56.5268 |
| GG663368.1 | 1769553 | 46800953 | 26.4479 | 46.6053 |
| GG663367.1 | 2225114 | 78295840 | 35.1873 | 91.8856 |
| GG663366.1 | 2702831 | 163103242 | 60.3453 | 75.8988 |
| GG663365.1 | 2818386 | 93211225 | 33.0726 | 92.6327 |
| GG663364.1 | 2928037 | 83342152 | 28.4635 | 46.2216 |
| GG663363.1 | 3777229 | 116530905 | 30.8509 | 69.9206 |
| GG663450.1 | 4245 | 8239 | 1.9409 | 6.3446 |
| GG663449.1 | 40201 | 88551 | 2.2027 | 6.3342 |
