BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950198_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR950198/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 16,007,597 number of mapped reads = 11,080,836 (69.22%) number of mapped paired reads (first in pair) = 5,535,558 number of mapped paired reads (second in pair) = 5,545,278 number of mapped paired reads (both in pair) = 8,714,371 number of mapped paired reads (singletons) = 2,366,465 number of mapped bases = 1,530,548,012 bp number of sequenced bases = 881,008,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,586,306 duplication rate = 43.36% >>>>>>> Insert size mean insert size = 2,384.0358 std insert size = 26,113.8661 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 32.3691 >>>>>>> ACTG content number of A's = 220,085,608 bp (24.98%) number of C's = 218,681,914 bp (24.82%) number of T's = 218,383,639 bp (24.79%) number of G's = 223,857,167 bp (25.41%) number of N's = 649,391,401 bp (73.71%) GC percentage = 50.23% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 12,008,175 number of insertions = 160,395 mapped reads with insertion percentage = 1.44% number of deletions = 124,823 mapped reads with deletion percentage = 1.12% homopolymer indels = 63.36% >>>>>>> Coverage mean coverageData = 50.2094X std coverageData = 206.1942X There is a 57.67% of reference with a coverageData >= 1X There is a 51.43% of reference with a coverageData >= 2X There is a 47.5% of reference with a coverageData >= 3X There is a 44.61% of reference with a coverageData >= 4X There is a 42.25% of reference with a coverageData >= 5X There is a 40.21% of reference with a coverageData >= 6X There is a 38.4% of reference with a coverageData >= 7X There is a 36.76% of reference with a coverageData >= 8X There is a 35.27% of reference with a coverageData >= 9X There is a 33.89% of reference with a coverageData >= 10X There is a 32.59% of reference with a coverageData >= 11X There is a 31.37% of reference with a coverageData >= 12X There is a 30.22% of reference with a coverageData >= 13X There is a 29.14% of reference with a coverageData >= 14X There is a 28.1% of reference with a coverageData >= 15X There is a 27.12% of reference with a coverageData >= 16X There is a 26.2% of reference with a coverageData >= 17X There is a 25.31% of reference with a coverageData >= 18X There is a 24.47% of reference with a coverageData >= 19X There is a 23.67% of reference with a coverageData >= 20X There is a 22.91% of reference with a coverageData >= 21X There is a 22.19% of reference with a coverageData >= 22X There is a 21.51% of reference with a coverageData >= 23X There is a 20.85% of reference with a coverageData >= 24X There is a 20.23% of reference with a coverageData >= 25X There is a 19.64% of reference with a coverageData >= 26X There is a 19.08% of reference with a coverageData >= 27X There is a 18.54% of reference with a coverageData >= 28X There is a 18.03% of reference with a coverageData >= 29X There is a 17.54% of reference with a coverageData >= 30X There is a 17.07% of reference with a coverageData >= 31X There is a 16.62% of reference with a coverageData >= 32X There is a 16.18% of reference with a coverageData >= 33X There is a 15.77% of reference with a coverageData >= 34X There is a 15.37% of reference with a coverageData >= 35X There is a 14.98% of reference with a coverageData >= 36X There is a 14.62% of reference with a coverageData >= 37X There is a 14.26% of reference with a coverageData >= 38X There is a 13.92% of reference with a coverageData >= 39X There is a 13.59% of reference with a coverageData >= 40X There is a 13.28% of reference with a coverageData >= 41X There is a 12.98% of reference with a coverageData >= 42X There is a 12.69% of reference with a coverageData >= 43X There is a 12.4% of reference with a coverageData >= 44X There is a 12.13% of reference with a coverageData >= 45X There is a 11.87% of reference with a coverageData >= 46X There is a 11.61% of reference with a coverageData >= 47X There is a 11.36% of reference with a coverageData >= 48X There is a 11.13% of reference with a coverageData >= 49X There is a 10.9% of reference with a coverageData >= 50X There is a 10.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 70775 29.403822185292896 40.59120831634451 GG663447.1 5093 1059 0.2079324563125859 0.4604953790503837 GG663446.1 5267 0 0.0 0.0 GG663445.1 5726 0 0.0 0.0 GG663444.1 6104 0 0.0 0.0 GG663443.1 6704 0 0.0 0.0 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 395 0.042236954662104365 0.2737156606587173 GG663437.1 9532 3700 0.38816617708770457 2.0372602344350814 GG663436.1 9723 154175 15.856731461483081 18.296805027066743 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 31129 2.802899333693499 6.968761868068768 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 917 0.07739049708836189 0.2968831040801618 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 1039 0.08426601784266018 0.38074580070911057 GG663427.1 12422 65 0.00523265174690066 0.07214756477246005 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 1296 0.08485007201780805 0.1252188004827482 GG663424.1 15855 0 0.0 0.0 GG663423.1 16334 239 0.014632055834455737 0.12007480491973786 GG663422.1 16757 77460 4.622545801754491 10.837122859064323 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 0 0.0 0.0 GG663419.1 17524 248 0.014152020086738187 0.12065177904592374 GG663418.1 17580 0 0.0 0.0 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 240 0.011814512159102097 0.12806535177473008 GG663415.1 20172 18466 0.9154273250049574 0.9136483431675296 GG663414.1 21124 0 0.0 0.0 GG663413.1 21814 160 0.007334739158338681 0.1201345555583323 GG663412.1 22664 0 0.0 0.0 GG663411.1 23942 0 0.0 0.0 GG663410.1 24438 927 0.03793272771912595 0.635445252313909 GG663409.1 30061 0 0.0 0.0 GG663408.1 29608 0 0.0 0.0 GG663407.1 31202 1288574 41.29780142298571 76.97207585937207 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 389 0.011641129997605937 0.16324233771325733 GG663404.1 33436 0 0.0 0.0 GG663403.1 34148 0 0.0 0.0 GG663402.1 35232 35085 0.9958276566757494 2.1028587488746426 GG663401.1 36230 965720 26.65525807341982 36.62355034763929 GG663400.1 40055 0 0.0 0.0 GG663399.1 47125 0 0.0 0.0 GG663398.1 49169 0 0.0 0.0 GG663397.1 50304 9625 0.19133667302798982 0.22649620384226837 GG663396.1 51171 67 0.001309335365734498 0.03616104266520166 GG663395.1 53466 0 0.0 0.0 GG663394.1 53864 335 0.006219367295410664 0.06662524899257445 GG663393.1 55852 1026474 18.37846451335673 103.40975955246682 GG663392.1 60589 156 0.0025747247850269853 0.06595905814638202 GG663391.1 76172 158 0.002074253006354041 0.04549670846137852 GG663390.1 87620 214 0.0024423647569048164 0.0294806732629853 GG663389.1 88906 80 8.998267833442063E-4 0.029983613776597758 GG663388.1 95026 23164 0.24376486435291395 0.24619738136004463 GG663387.1 113334 2492 0.021988105952317927 0.37194773600943004 GG663386.1 144210 54088 0.37506414256986337 0.3990776039116336 GG663385.1 156336 156730 1.0025202128748336 2.103339687169235 GG663384.1 204511 3249209 15.887697972236213 35.98631657625094 GG663383.1 258077 7514139 29.11588014429802 72.81586953834851 GG663382.1 261570 7227581 27.631536491187827 53.62301014654899 GG663381.1 280411 6386095 22.774053086362517 39.9751945631105 GG663380.1 351122 18843875 53.66759986557379 152.94489460070855 GG663379.1 441739 18308788 41.44707168712747 115.83313293716638 GG663378.1 530530 18154035 34.218677548866225 97.86646861938078 GG663377.1 695743 26572912 38.19357435144874 88.04174792698728 GG663376.1 920403 39197586 42.58741659903325 126.50939058544223 GG663375.1 915096 28502269 31.146752908984414 87.1342131757086 GG663374.1 967551 69041384 71.35684217162712 131.44829651031546 GG663373.1 1058542 200423523 189.33922602976546 679.6559980662537 GG663372.1 1221551 82238346 67.32289196275882 218.79700828774423 GG663371.1 1250234 39006681 31.199504252803877 87.25885407208098 GG663370.1 1327755 114947019 86.57246178700137 517.4924351469865 GG663369.1 1498222 76568443 51.10620655683871 136.32789655100476 GG663368.1 1769553 51608073 29.1644686539482 67.48077067485116 GG663367.1 2225114 88642327 39.83720699254061 120.79370796256147 GG663366.1 2702831 203145421 75.16023791350625 186.53624611415088 GG663365.1 2818386 137235732 48.693022176522305 158.81526665006538 GG663364.1 2928037 116302049 39.72014322223387 96.1460149148571 GG663363.1 3777229 172801664 45.748262549080295 127.92010747590362 GG663450.1 4245 6344 1.4944640753828033 5.2419234586014145 GG663449.1 40201 698876 17.384542673067834 42.287581827343566