BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237816.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,295,538 number of mapped reads = 2,201,326 (95.9%) number of supplementary alignments = 13,656 (0.59%) number of secondary alignments = 0 number of mapped bases = 160,538,806 bp number of sequenced bases = 160,468,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,440 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1982 >>>>>>> ACTG content number of A's = 48,993,000 bp (30.53%) number of C's = 31,783,647 bp (19.81%) number of T's = 47,655,197 bp (29.7%) number of G's = 31,765,293 bp (19.8%) number of N's = 270,980 bp (0.17%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,363,429 number of insertions = 12,199 mapped reads with insertion percentage = 0.55% number of deletions = 38,712 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.6576X There is a 3.86% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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% 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 11772253 0.047230586438538905 1.6589603258701684 chr2 243199373 14948156 0.06146461570030446 0.5726373991441959 chr3 198022430 13290508 0.06711617466768789 0.3365831885671995 chr4 191154276 10464437 0.05474341050053204 0.34723256902128513 chr5 180915260 9513441 0.052585066621798515 0.2938907822817943 chr6 171115067 10133688 0.05922148281658914 0.4306827320049907 chr7 159138663 10313990 0.06481134003243448 0.8445214816738275 chr8 146364022 7583556 0.05181297901201431 0.4717591475764985 chr9 141213431 6279390 0.04446737081262476 0.4911789029070418 chr10 135534747 7385521 0.05449171643047373 0.6300453769223526 chr11 135006516 6531000 0.04837544285640258 0.407158438480252 chr12 133851895 7873392 0.05882167002566531 0.31496934592913195 chr13 115169878 5069151 0.04401455561149418 0.26196521375329956 chr14 107349540 4673907 0.04353914325110289 0.2783411922679122 chr15 102531392 4180045 0.04076844094733445 0.2534333070047212 chr16 90354753 3751456 0.041519188260079685 0.32490177148562294 chr17 81195210 3348786 0.041243639864962475 0.318855579978573 chr18 78077248 4602290 0.05894534090135964 1.0010470608687965 chr19 59128983 2304899 0.03898086662508638 0.8868609949984393 chr20 63025520 2708334 0.04297202149224631 0.2804698325084342 chr21 48129895 1985507 0.04125309228287325 0.3074924113426347 chr22 51304566 1228588 0.023946952401858346 0.192198191163583 chrMT 16571 338525 20.428761088648844 13.220685247700025 chrX 155270560 9804866 0.0631469739015561 0.35901231872964806 chrY 59373566 453120 0.007631679053941277 0.24311314608089515