BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751189.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,381,905 number of mapped reads = 4,979,199 (92.52%) number of supplementary alignments = 125,034 (2.32%) number of secondary alignments = 0 number of mapped bases = 490,245,339 bp number of sequenced bases = 490,110,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,509 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3506 >>>>>>> ACTG content number of A's = 143,426,747 bp (29.26%) number of C's = 101,764,154 bp (20.76%) number of T's = 143,910,207 bp (29.36%) number of G's = 101,006,834 bp (20.61%) number of N's = 2,758 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,683,792 number of insertions = 76,174 mapped reads with insertion percentage = 1.51% number of deletions = 61,773 mapped reads with deletion percentage = 1.22% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.1584X std coverageData = 1.3244X There is a 12.46% of reference with a coverageData >= 1X There is a 2.41% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 58568019 0.23497642158331875 3.8105916914526423 chr2 243199373 36673897 0.15079766262390817 0.5463220504417817 chr3 198022430 32621077 0.16473425257936689 0.49239440485863906 chr4 191154276 22831383 0.11943956200069519 0.4441863238757953 chr5 180915260 40162568 0.2219965745288706 0.5529281859999302 chr6 171115067 27907925 0.16309449243297786 0.8910546091860218 chr7 159138663 27535205 0.17302649451063945 0.7105564579700372 chr8 146364022 24238649 0.1656052400637091 0.5229765629938011 chr9 141213431 21208496 0.15018752713401604 0.6300094933651248 chr10 135534747 23935149 0.1765978800993372 1.5415700170189763 chr11 135006516 22165353 0.16417987558467179 0.6911312286197148 chr12 133851895 25846454 0.19309740814651896 0.510652730370175 chr13 115169878 14604557 0.126808825828573 0.41146921881695564 chr14 107349540 10332894 0.09625466490121895 0.3670156590496381 chr15 102531392 11785507 0.11494535254139532 0.3916761045887227 chr16 90354753 13456282 0.148927218029139 0.7540675531236718 chr17 81195210 13406371 0.16511283116331615 0.6901246365323519 chr18 78077248 10060054 0.128847446057525 1.1252692486318947 chr19 59128983 9164035 0.15498380887085442 2.534397718382831 chr20 63025520 8691498 0.13790442347798162 0.43825294892826216 chr21 48129895 6096047 0.126658223542769 0.45136866460350816 chr22 51304566 5553713 0.10824987779840102 0.3856370831637316 chrMT 16571 1473222 88.90362681793495 37.14784301734533 chrX 155270560 20941504 0.1348710534695051 0.4894882414713383 chrY 59373566 985480 0.01659795876164824 0.5807291931855937