BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716274.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 643,412 number of mapped reads = 560,738 (87.15%) number of supplementary alignments = 2,603 (0.4%) number of secondary alignments = 0 number of mapped bases = 31,815,003 bp number of sequenced bases = 31,806,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,166 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6022 >>>>>>> ACTG content number of A's = 7,534,372 bp (23.69%) number of C's = 5,854,141 bp (18.41%) number of T's = 10,231,283 bp (32.17%) number of G's = 8,185,984 bp (25.74%) number of N's = 684 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 156,287 number of insertions = 2,030 mapped reads with insertion percentage = 0.36% number of deletions = 5,057 mapped reads with deletion percentage = 0.9% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0103X std coverageData = 0.1152X There is a 0.98% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3578706 0.014357861920833489 0.15322879932417505 chr2 243199373 2661980 0.010945669666673031 0.12624213186102792 chr3 198022430 2129853 0.010755614906856763 0.10741847634462291 chr4 191154276 2023215 0.010584199539433792 0.10998037803165803 chr5 180915260 1586163 0.008767436201899166 0.09726480305022411 chr6 171115067 1658249 0.009690841543486057 0.10434339859573508 chr7 159138663 1370067 0.008609265493200732 0.10412489142347156 chr8 146364022 1991146 0.013604067261830234 0.12677656632623216 chr9 141213431 1152458 0.008161107564902945 0.10695803152623158 chr10 135534747 1480364 0.01092239468304021 0.1252684782679014 chr11 135006516 995146 0.007371096073614699 0.09888539533187503 chr12 133851895 1445836 0.010801759661303263 0.10819605337163325 chr13 115169878 997710 0.008662942232169422 0.09590972326098908 chr14 107349540 1096492 0.01021422169112229 0.10766547078945682 chr15 102531392 903763 0.008814500440996647 0.09695766129834661 chr16 90354753 952042 0.010536711887198673 0.110505307611754 chr17 81195210 721292 0.008883430438815294 0.09839273320747488 chr18 78077248 780330 0.009994332792057425 0.16576323716805344 chr19 59128983 619941 0.010484553742451481 0.12420442430581524 chr20 63025520 1016200 0.01612362738141629 0.1327223451576968 chr21 48129895 402449 0.008361726116377357 0.09779472177264553 chr22 51304566 379261 0.007392343987472772 0.08862464894708968 chrMT 16571 4852 0.2928006758795486 0.6230796880548682 chrX 155270560 1770332 0.011401594738886753 0.11638843780869514 chrY 59373566 97156 0.0016363510994101315 0.05026764204196044