BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950093_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR950093/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 17,996,144 number of mapped reads = 16,998,173 (94.45%) number of mapped paired reads (first in pair) = 8,447,431 number of mapped paired reads (second in pair) = 8,550,742 number of mapped paired reads (both in pair) = 16,183,562 number of mapped paired reads (singletons) = 814,611 number of mapped bases = 2,191,378,231 bp number of sequenced bases = 1,356,798,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,598,144 duplication rate = 43.72% >>>>>>> Insert size mean insert size = 2,750.0481 std insert size = 30,218.206 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 38.2432 >>>>>>> ACTG content number of A's = 345,384,168 bp (25.46%) number of C's = 332,831,633 bp (24.53%) number of T's = 342,976,753 bp (25.28%) number of G's = 335,606,398 bp (24.74%) number of N's = 834,532,961 bp (61.51%) GC percentage = 49.27% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 4,405,954 number of insertions = 102,316 mapped reads with insertion percentage = 0.6% number of deletions = 38,317 mapped reads with deletion percentage = 0.22% homopolymer indels = 84.87% >>>>>>> Coverage mean coverageData = 71.8878X std coverageData = 302.6794X There is a 75.54% of reference with a coverageData >= 1X There is a 68.98% of reference with a coverageData >= 2X There is a 64.43% of reference with a coverageData >= 3X There is a 60.96% of reference with a coverageData >= 4X There is a 58.1% of reference with a coverageData >= 5X There is a 55.66% of reference with a coverageData >= 6X There is a 53.51% of reference with a coverageData >= 7X There is a 51.59% of reference with a coverageData >= 8X There is a 49.8% of reference with a coverageData >= 9X There is a 48.14% of reference with a coverageData >= 10X There is a 46.58% of reference with a coverageData >= 11X There is a 45.09% of reference with a coverageData >= 12X There is a 43.67% of reference with a coverageData >= 13X There is a 42.34% of reference with a coverageData >= 14X There is a 41.07% of reference with a coverageData >= 15X There is a 39.87% of reference with a coverageData >= 16X There is a 38.71% of reference with a coverageData >= 17X There is a 37.62% of reference with a coverageData >= 18X There is a 36.57% of reference with a coverageData >= 19X There is a 35.56% of reference with a coverageData >= 20X There is a 34.58% of reference with a coverageData >= 21X There is a 33.66% of reference with a coverageData >= 22X There is a 32.76% of reference with a coverageData >= 23X There is a 31.91% of reference with a coverageData >= 24X There is a 31.08% of reference with a coverageData >= 25X There is a 30.29% of reference with a coverageData >= 26X There is a 29.53% of reference with a coverageData >= 27X There is a 28.79% of reference with a coverageData >= 28X There is a 28.08% of reference with a coverageData >= 29X There is a 27.38% of reference with a coverageData >= 30X There is a 26.71% of reference with a coverageData >= 31X There is a 26.07% of reference with a coverageData >= 32X There is a 25.44% of reference with a coverageData >= 33X There is a 24.83% of reference with a coverageData >= 34X There is a 24.25% of reference with a coverageData >= 35X There is a 23.68% of reference with a coverageData >= 36X There is a 23.13% of reference with a coverageData >= 37X There is a 22.6% of reference with a coverageData >= 38X There is a 22.09% of reference with a coverageData >= 39X There is a 21.59% of reference with a coverageData >= 40X There is a 21.11% of reference with a coverageData >= 41X There is a 20.65% of reference with a coverageData >= 42X There is a 20.21% of reference with a coverageData >= 43X There is a 19.78% of reference with a coverageData >= 44X There is a 19.37% of reference with a coverageData >= 45X There is a 18.97% of reference with a coverageData >= 46X There is a 18.58% of reference with a coverageData >= 47X There is a 18.21% of reference with a coverageData >= 48X There is a 17.84% of reference with a coverageData >= 49X There is a 17.49% of reference with a coverageData >= 50X There is a 17.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 131512 54.63730785209805 57.81809464346682 GG663447.1 5093 80 0.015707834282348322 0.12434266453839006 GG663446.1 5267 560 0.10632238465919878 0.4537587392734495 GG663445.1 5726 2380 0.4156479217603912 1.6469129848624044 GG663444.1 6104 0 0.0 0.0 GG663443.1 6704 160 0.02386634844868735 0.15263271556390912 GG663442.1 7013 0 0.0 0.0 GG663441.1 7428 0 0.0 0.0 GG663440.1 7433 0 0.0 0.0 GG663439.1 7612 0 0.0 0.0 GG663438.1 9352 11424 1.221556886227545 4.66703738944725 GG663437.1 9532 91062 9.553294167016366 6.7295904409290515 GG663436.1 9723 475356 48.88984881209503 52.36199929037177 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 202473 18.23095623987034 37.75631626535691 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 481 0.04059414296565111 0.18740213226186192 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 1271438 103.11743714517438 232.86854008555494 GG663427.1 12422 401 0.03228143616164869 0.193376544487957 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 320 0.02095063506612544 0.1432190837718615 GG663424.1 15855 160 0.010091453800063072 0.09994806831682272 GG663423.1 16334 148865 9.113811681155871 22.479768853816143 GG663422.1 16757 475790 28.393507191024646 58.97661459453862 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 320 0.018575491960294885 0.19184872952152376 GG663419.1 17524 3938 0.22472038347409268 0.6472399027313521 GG663418.1 17580 160 0.009101251422070534 0.09906956214728097 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 308 0.015161957270847692 0.14298780133335032 GG663415.1 20172 1353 0.06707317073170732 0.29807449358833055 GG663414.1 21124 0 0.0 0.0 GG663413.1 21814 14534 0.66626936829559 1.8015380826946563 GG663412.1 22664 400 0.017649135192375574 0.17077050037470892 GG663411.1 23942 1035 0.043229471222120126 0.2098423474013044 GG663410.1 24438 0 0.0 0.0 GG663409.1 30061 236 0.007850703569408868 0.08825570816028921 GG663408.1 29608 641 0.02164955417454742 0.1847569698019333 GG663407.1 31202 4464222 143.0748669957054 223.09269875332825 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 227 0.006793152980608092 0.07646272075315504 GG663404.1 33436 39010 1.1667065438449575 1.162640182606541 GG663403.1 34148 1196 0.035024013119362776 0.39586660039858207 GG663402.1 35232 37114 1.0534173478655768 2.2151504350860023 GG663401.1 36230 2286170 63.10157328181065 106.44500409903952 GG663400.1 40055 0 0.0 0.0 GG663399.1 47125 0 0.0 0.0 GG663398.1 49169 799 0.016250076267566964 0.1486183590472561 GG663397.1 50304 2388 0.047471374045801526 0.3283856231645433 GG663396.1 51171 2545 0.04973520157901937 0.3814713497625683 GG663395.1 53466 3302 0.061758874798937644 0.4379945816304911 GG663394.1 53864 216887 4.026566909252933 14.851660677911303 GG663393.1 55852 862437 15.441470314402348 84.52383216599468 GG663392.1 60589 2272 0.037498555843469936 0.2931688878172047 GG663391.1 76172 160 0.002100509373523079 0.0477482125746932 GG663390.1 87620 5961 0.0680324126911664 0.677848035500921 GG663389.1 88906 640 0.00719861426675365 0.10602361097231258 GG663388.1 95026 3815 0.040146907162250334 0.3140227370703346 GG663387.1 113334 125527 1.1075846612666984 4.923805216926594 GG663386.1 144210 15160 0.10512447125719437 0.768603780781065 GG663385.1 156336 240751 1.5399588066728074 12.229836237953407 GG663384.1 204511 5772029 28.223562546757876 62.153569004645725 GG663383.1 258077 18741733 72.62070234852389 408.0893124294534 GG663382.1 261570 9201784 35.17904958519708 81.31048739244189 GG663381.1 280411 10469971 37.33794679951928 51.39032238351161 GG663380.1 351122 28309263 80.62514738466972 173.52118014177498 GG663379.1 441739 26852162 60.787392555332445 154.7338392935113 GG663378.1 530530 26001703 49.01080617495712 111.18645462846027 GG663377.1 695743 31427848 45.17163377856479 116.02550531697551 GG663376.1 920403 56520944 61.40890892359108 281.02658605436386 GG663375.1 915096 43007515 46.99781771529982 97.01099984450082 GG663374.1 967551 47780003 49.38241291673514 127.23400725013829 GG663373.1 1058542 220683288 208.47853746001576 1164.7895162676416 GG663372.1 1221551 110515570 90.47151531127231 251.922411708215 GG663371.1 1250234 70873685 56.688335943511376 188.9351251401427 GG663370.1 1327755 77238970 58.172607145143495 143.66621316013584 GG663369.1 1498222 83817286 55.94450355154309 181.44660674900484 GG663368.1 1769553 91667004 51.80235008502147 128.28821735675936 GG663367.1 2225114 137776255 61.91873989377623 207.93777113940595 GG663366.1 2702831 373493365 138.1859853612749 190.35276711959474 GG663365.1 2818386 291359512 103.37814337709597 437.67017307205555 GG663364.1 2928037 163657072 55.89310244371912 116.42759921733202 GG663363.1 3777229 254763629 67.44722890775222 219.21535526294846 GG663450.1 4245 14764 3.4779740871613662 11.210956555292077 GG663449.1 40201 286906 7.136787642098455 15.972742616167812