BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237319.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 = 3,038,373 number of mapped reads = 2,658,723 (87.5%) number of supplementary alignments = 27,185 (0.89%) number of secondary alignments = 0 number of mapped bases = 164,986,607 bp number of sequenced bases = 164,909,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 818,893 duplication rate = 20.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.595 >>>>>>> ACTG content number of A's = 41,568,150 bp (25.21%) number of C's = 28,757,590 bp (17.44%) number of T's = 54,896,022 bp (33.29%) number of G's = 39,670,016 bp (24.06%) number of N's = 17,515 bp (0.01%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 999,297 number of insertions = 13,421 mapped reads with insertion percentage = 0.5% number of deletions = 43,456 mapped reads with deletion percentage = 1.61% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 0.0533X std coverageData = 0.7345X There is a 2.32% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 16982442 0.06813400075741437 0.6659928389941562 chr2 243199373 19428008 0.07988510726958166 1.4981600199090044 chr3 198022430 17012935 0.0859141815399397 0.55842653260363 chr4 191154276 7588703 0.03969936304223715 0.6271156537449993 chr5 180915260 7738868 0.04277620362151872 0.4031407348087032 chr6 171115067 13110038 0.07661533393783494 0.6694629260554423 chr7 159138663 17704601 0.11125266900099569 1.1517486685841907 chr8 146364022 5830478 0.03983545901738065 0.739773275311947 chr9 141213431 7484298 0.052999901971080926 0.4957197334056761 chr10 135534747 5796595 0.04276833157773187 0.8529134011053188 chr11 135006516 5720808 0.04237431028884561 0.4397598264406442 chr12 133851895 3050634 0.022791115508674718 0.32585425169152393 chr13 115169878 5854025 0.05082947990966874 0.49976336323993326 chr14 107349540 4561918 0.04249592499418255 0.41297021034671433 chr15 102531392 5155787 0.05028496053189251 0.4440388235124506 chr16 90354753 2186165 0.02419535140558682 0.3525769852380217 chr17 81195210 2494833 0.030726356887308993 0.3828579623762929 chr18 78077248 1741069 0.02229931311103588 1.2741246979958167 chr19 59128983 2771118 0.04686564624323067 0.4973039332373434 chr20 63025520 3004013 0.04766343855631814 0.44538532988525614 chr21 48129895 2819653 0.05858423335434245 0.579347895956986 chr22 51304566 1488297 0.02900905545132182 0.3373297191389142 chrMT 16571 21803 1.3157323034216402 2.213544553190325 chrX 155270560 4859963 0.03129996439762953 0.3824083593241037 chrY 59373566 579555 0.009761162063265662 0.5011329199820092