BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068182.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 = 1,544,993 number of mapped reads = 1,365,695 (88.39%) number of supplementary alignments = 13,443 (0.87%) number of secondary alignments = 0 number of mapped bases = 91,296,891 bp number of sequenced bases = 91,256,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,532 duplication rate = 8.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8337 >>>>>>> ACTG content number of A's = 25,902,400 bp (28.38%) number of C's = 16,850,379 bp (18.46%) number of T's = 28,997,318 bp (31.78%) number of G's = 19,409,578 bp (21.27%) number of N's = 96,863 bp (0.11%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 760,920 number of insertions = 6,275 mapped reads with insertion percentage = 0.46% number of deletions = 24,080 mapped reads with deletion percentage = 1.74% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0295X std coverageData = 0.3326X There is a 1.59% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 6623051 0.02657185355618432 0.48532032495924504 chr2 243199373 5371409 0.022086442632399384 0.28794351402394097 chr3 198022430 7240691 0.03656500427754573 0.3156741419673709 chr4 191154276 2584597 0.013521000178934005 0.19362675083250155 chr5 180915260 1917621 0.010599553625271855 0.16261874127799997 chr6 171115067 9114679 0.05326637308916812 0.3978567318281134 chr7 159138663 6042259 0.03796851680223052 0.4119333206403241 chr8 146364022 2663210 0.018195796778527992 0.4040214274204992 chr9 141213431 2839737 0.020109539014033305 0.25570197314006643 chr10 135534747 6243504 0.04606570741597356 0.3788493634580856 chr11 135006516 3363663 0.0249148196669263 0.27537668989312597 chr12 133851895 1478168 0.011043310219851575 0.1733078145480974 chr13 115169878 1647888 0.01430832461244771 0.19510924939471586 chr14 107349540 2460299 0.022918579809471006 0.24793198843087094 chr15 102531392 2776860 0.027083022534210792 0.26305328851875015 chr16 90354753 4099482 0.045370961281915076 0.34487209680959635 chr17 81195210 1806116 0.022244120065703383 0.23921777435205688 chr18 78077248 3106730 0.03979046495081384 0.4156873627925244 chr19 59128983 845072 0.014292009723894626 0.3123457737674092 chr20 63025520 597136 0.009474511277336546 0.16351853055454507 chr21 48129895 2814349 0.05847403157642459 0.4025411351236346 chr22 51304566 1112519 0.021684600158200344 0.2295426610597107 chrMT 16571 4621 0.2788606601894877 0.7676231899390517 chrX 155270560 14206594 0.09149573492875919 0.5317066044138943 chrY 59373566 336636 0.005669795881891278 0.13645151151734444