BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237862.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 = 1,265,640 number of mapped reads = 1,085,494 (85.77%) number of supplementary alignments = 10,108 (0.8%) number of secondary alignments = 0 number of mapped bases = 69,967,511 bp number of sequenced bases = 69,941,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,683 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0863 >>>>>>> ACTG content number of A's = 18,988,036 bp (27.15%) number of C's = 12,605,972 bp (18.02%) number of T's = 22,519,235 bp (32.2%) number of G's = 15,764,695 bp (22.54%) number of N's = 63,622 bp (0.09%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 534,930 number of insertions = 5,384 mapped reads with insertion percentage = 0.49% number of deletions = 15,397 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2406X There is a 1.73% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5418608 0.021739596789209205 0.36653058824080414 chr2 243199373 6158716 0.025323733050907165 0.2588707634281801 chr3 198022430 4701074 0.023740108633148276 0.19404813032121387 chr4 191154276 5048838 0.0264123727998635 0.21545015823651315 chr5 180915260 4842949 0.026769157007540435 0.2064647468867784 chr6 171115067 4235783 0.024754003690393902 0.21752445160751147 chr7 159138663 3773350 0.023711082705275714 0.27130137368839063 chr8 146364022 3741603 0.02556367985022986 0.2696754810938919 chr9 141213431 3083898 0.021838560101269687 0.23108154174658813 chr10 135534747 3154216 0.023272379001083757 0.2566784582396151 chr11 135006516 3150933 0.023339117943018396 0.21974657191086408 chr12 133851895 2973049 0.022211482325296926 0.1880181249190802 chr13 115169878 2276878 0.019769735277482884 0.17649189825629205 chr14 107349540 1869065 0.017411020112428986 0.17183344259020247 chr15 102531392 1943716 0.01895727700644111 0.1722792368707095 chr16 90354753 1839530 0.02035897325733379 0.19145538550893829 chr17 81195210 1569891 0.019334773566076126 0.18924599242954546 chr18 78077248 1909073 0.024451079525753778 0.34418740220504007 chr19 59128983 1198830 0.020274828674120778 0.3057567124768515 chr20 63025520 1319886 0.020942088220771524 0.18596666955852845 chr21 48129895 932933 0.01938364918518937 0.1838760827859762 chr22 51304566 675267 0.013161927926648867 0.13973488948113946 chrMT 16571 231808 13.988775571782028 7.801085949473676 chrX 155270560 3725324 0.023992468372626467 0.20877803564755368 chrY 59373566 192293 0.003238697167018737 0.092830097802701