BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716833.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 = 630,374 number of mapped reads = 485,668 (77.04%) number of supplementary alignments = 3,008 (0.48%) number of secondary alignments = 0 number of mapped bases = 28,858,262 bp number of sequenced bases = 28,850,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,739 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5591 >>>>>>> ACTG content number of A's = 7,321,768 bp (25.38%) number of C's = 5,399,930 bp (18.72%) number of T's = 9,211,332 bp (31.93%) number of G's = 6,916,772 bp (23.97%) number of N's = 216 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 142,216 number of insertions = 1,986 mapped reads with insertion percentage = 0.41% number of deletions = 5,153 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.3% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1179X There is a 0.86% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 2275464 0.00912922098597299 0.14351081171577607 chr2 243199373 2395872 0.009851472766749279 0.13997371389130936 chr3 198022430 1923585 0.009713975330976395 0.1048663543533648 chr4 191154276 1831907 0.009583395351302527 0.1129372663278454 chr5 180915260 1732780 0.009577854294878166 0.10435666082985412 chr6 171115067 1588354 0.00928237371405757 0.10674136042534288 chr7 159138663 1564722 0.00983244404912463 0.1281966909721299 chr8 146364022 1439828 0.00983730824232201 0.1475002891784997 chr9 141213431 1220151 0.008640474148666496 0.10529651079752825 chr10 135534747 1407648 0.010385882817193734 0.13011695461053585 chr11 135006516 1326054 0.009822148139872004 0.1138890442905494 chr12 133851895 1283202 0.009586730169191851 0.10460843863577933 chr13 115169878 902851 0.007839298049790415 0.09442003222142605 chr14 107349540 862422 0.008033774527585308 0.09556060629483927 chr15 102531392 828299 0.008078491707203195 0.09533540314892812 chr16 90354753 887460 0.009821951480515918 0.10833721737918403 chr17 81195210 815558 0.0100444102552355 0.10995028598948585 chr18 78077248 755239 0.009672971567850342 0.14724538982562907 chr19 59128983 599139 0.01013274657539772 0.13024268954017074 chr20 63025520 648636 0.010291640592572659 0.11037356975443818 chr21 48129895 386223 0.00802459677088429 0.1029154516392345 chr22 51304566 361372 0.007043661571954434 0.08974067693278825 chrMT 16571 27919 1.6848108140727778 1.544338095622561 chrX 155270560 1693094 0.010904153369447498 0.11355286182545363 chrY 59373566 100483 0.0016923861369552908 0.06596808432307126