BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524769.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 = 1,476,692 number of mapped reads = 1,347,216 (91.23%) number of supplementary alignments = 5,055 (0.34%) number of secondary alignments = 0 number of mapped bases = 77,065,170 bp number of sequenced bases = 77,039,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,405 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5169 >>>>>>> ACTG content number of A's = 18,507,041 bp (24.02%) number of C's = 13,550,404 bp (17.59%) number of T's = 25,682,787 bp (33.34%) number of G's = 19,289,188 bp (25.04%) number of N's = 10,127 bp (0.01%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 393,796 number of insertions = 5,524 mapped reads with insertion percentage = 0.41% number of deletions = 15,658 mapped reads with deletion percentage = 1.15% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2288X There is a 2.22% of reference with a coverageData >= 1X There is a 0.19% 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 6210818 0.02491796399576473 0.30167827471509406 chr2 243199373 6444655 0.02649947210184625 0.36376274142968007 chr3 198022430 5025765 0.02537977642229721 0.17879030420093628 chr4 191154276 4923594 0.025757174273203284 0.20002000416521046 chr5 180915260 4581669 0.025324944949364693 0.174367755522162 chr6 171115067 4387236 0.025639098163109154 0.19313057691270674 chr7 159138663 4222943 0.026536247825583403 0.2721041164353745 chr8 146364022 3817104 0.026079523832708014 0.21603440653904568 chr9 141213431 3311034 0.023447019002038126 0.19783375151626503 chr10 135534747 3748244 0.0276552255636704 0.26718028600884086 chr11 135006516 3461769 0.025641495703807363 0.2080752316651573 chr12 133851895 3494701 0.026108715158646056 0.18140683448167227 chr13 115169878 2405459 0.02088618171497933 0.15837442047960695 chr14 107349540 2337159 0.02177148593277624 0.16452712195943284 chr15 102531392 2266804 0.022108389984601007 0.16353741021368376 chr16 90354753 2329582 0.025782617102611084 0.18917080293450353 chr17 81195210 2191966 0.026996247685054327 0.18636537329011754 chr18 78077248 2016746 0.025830136840888654 0.30342352225039604 chr19 59128983 1663805 0.02813856954042318 0.24983523725916523 chr20 63025520 1658926 0.026321496435094863 0.1844112800074716 chr21 48129895 1034370 0.021491216633653575 0.17870049466287746 chr22 51304566 961894 0.0187487016262841 0.15282200041449845 chrMT 16571 39109 2.360086898799107 2.22375035194206 chrX 155270560 4272051 0.027513593046872505 0.19262945203373014 chrY 59373566 257767 0.004341443800091105 0.12280832245253838