BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234064.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 = 3,963,882 number of mapped reads = 3,732,414 (94.16%) number of supplementary alignments = 38,480 (0.97%) number of secondary alignments = 0 number of mapped bases = 257,179,067 bp number of sequenced bases = 257,095,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 585,989 duplication rate = 6.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0705 >>>>>>> ACTG content number of A's = 64,686,083 bp (25.16%) number of C's = 45,388,538 bp (17.65%) number of T's = 70,764,704 bp (27.52%) number of G's = 76,200,045 bp (29.64%) number of N's = 55,716 bp (0.02%) GC percentage = 47.29% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,553,554 number of insertions = 16,109 mapped reads with insertion percentage = 0.43% number of deletions = 51,370 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.0831X std coverageData = 49.2861X There is a 4.52% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 34790825 0.1395816983741838 1.3368985136059781 chr2 243199373 36542063 0.15025558063424777 175.82843972802127 chr3 198022430 24173637 0.12207524672836305 0.5303458826194616 chr4 191154276 7161040 0.037462096845795906 0.2976341479042842 chr5 180915260 7964618 0.04402402539177734 0.31629773740111805 chr6 171115067 5979051 0.03494169803293827 0.3151395612359939 chr7 159138663 2811608 0.01766766131496279 0.2882851447815899 chr8 146364022 7028926 0.04802359148069872 0.7161936872603877 chr9 141213431 1959995 0.013879664180101963 0.35450366013990553 chr10 135534747 20847649 0.1538177438734585 0.7702062870710686 chr11 135006516 14380007 0.10651342932218175 0.7244687110665381 chr12 133851895 8443008 0.06307723921278813 0.378841286677916 chr13 115169878 9784684 0.0849587076926486 0.4415453911832541 chr14 107349540 7361262 0.06857283226365013 0.5019063870439192 chr15 102531392 4451642 0.043417356510677234 0.3118952174103931 chr16 90354753 5135926 0.056841791156243875 0.40412578154940293 chr17 81195210 9540025 0.11749492365374756 0.6524690023846893 chr18 78077248 3282974 0.04204776787214631 0.8187176258968109 chr19 59128983 5355058 0.09056570447017498 0.8448284122070882 chr20 63025520 9681530 0.1536128539677261 0.6291793096253194 chr21 48129895 6513375 0.1353290922409035 0.5803227258331275 chr22 51304566 796517 0.01552526533408352 0.18232667608054234 chrMT 16571 70166 4.2342646792589465 3.7504333586963714 chrX 155270560 22442092 0.1445353967938288 0.6156507937331794 chrY 59373566 681389 0.011476302433982153 0.17544488421634105