BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716320.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 = 2,272,474 number of mapped reads = 1,586,997 (69.84%) number of supplementary alignments = 6,729 (0.3%) number of secondary alignments = 0 number of mapped bases = 91,562,475 bp number of sequenced bases = 91,536,449 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,687 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7914 >>>>>>> ACTG content number of A's = 23,530,346 bp (25.71%) number of C's = 17,049,527 bp (18.63%) number of T's = 29,459,226 bp (32.18%) number of G's = 21,495,013 bp (23.48%) number of N's = 2,337 bp (0%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 460,122 number of insertions = 5,716 mapped reads with insertion percentage = 0.36% number of deletions = 16,428 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2874X There is a 2.65% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 9309834 0.037351297110710106 0.531585770605176 chr2 243199373 8541135 0.035119889063200835 0.37836500270015766 chr3 198022430 6734852 0.034010551228969364 0.202319551144019 chr4 191154276 4516764 0.023628893344766193 0.17908387928718347 chr5 180915260 4367833 0.02414297721485739 0.17182428281620113 chr6 171115067 7124070 0.04163321281345728 0.2764159489029007 chr7 159138663 5719388 0.03593965094453508 0.4457845976259029 chr8 146364022 5793309 0.03958150999704012 0.2555957856684407 chr9 141213431 3596496 0.02546851226920476 0.23026273229522287 chr10 135534747 4755685 0.03508830838781143 0.27912134075183187 chr11 135006516 3204130 0.02373315077621883 0.22537546693724902 chr12 133851895 3978204 0.02972093895271337 0.19131231643432958 chr13 115169878 2048601 0.01778764582871226 0.14550993178221294 chr14 107349540 2146336 0.019993900299898816 0.16718323040707025 chr15 102531392 2882193 0.028110346926724646 0.18706560491014979 chr16 90354753 2062282 0.02282427798789954 0.18161720788918242 chr17 81195210 2051574 0.0252671801698647 0.18183390600228977 chr18 78077248 1884177 0.02413221582809886 0.3980411284262226 chr19 59128983 2150964 0.03637749020645256 0.34074607949881836 chr20 63025520 1478871 0.02346463781655431 0.1707176686478841 chr21 48129895 935341 0.019433680459930363 0.1676277493257167 chr22 51304566 1509912 0.02943036298172759 0.18768543139162847 chrMT 16571 48751 2.941946774485547 2.280104358019398 chrX 155270560 4498380 0.02897123575776374 0.2134289799637154 chrY 59373566 223393 0.0037624992913513062 0.08936735703086637