BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068945.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 = 2,391,884 number of mapped reads = 2,042,051 (85.37%) number of supplementary alignments = 12,526 (0.52%) number of secondary alignments = 0 number of mapped bases = 135,367,699 bp number of sequenced bases = 135,308,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,615 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9134 >>>>>>> ACTG content number of A's = 37,322,010 bp (27.58%) number of C's = 23,510,764 bp (17.38%) number of T's = 44,869,811 bp (33.16%) number of G's = 29,272,362 bp (21.63%) number of N's = 334,041 bp (0.25%) GC percentage = 39.01% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 1,429,764 number of insertions = 12,263 mapped reads with insertion percentage = 0.6% number of deletions = 35,390 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0437X std coverageData = 0.4288X There is a 3.75% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 15621692 0.06267463622487825 0.8938290382073321 chr2 243199373 8115844 0.03337115511395665 0.3370946740709956 chr3 198022430 8883054 0.044858827356072745 0.2425195210489649 chr4 191154276 3853133 0.020157189682746098 0.20282725139925806 chr5 180915260 7477059 0.04132906754245054 0.22957652857199723 chr6 171115067 8145761 0.04760399620449554 0.31459048873035916 chr7 159138663 9020565 0.05668367969133937 0.4883828684797494 chr8 146364022 10106087 0.06904761745342035 0.7239968876018269 chr9 141213431 7415712 0.0525142116262298 0.3450318703934043 chr10 135534747 8280349 0.0610939200705484 0.4773402283611604 chr11 135006516 4345719 0.03218895745743117 0.3142526513379591 chr12 133851895 8340686 0.06231279728987027 0.28277734458449816 chr13 115169878 4433206 0.038492755892300244 0.21925293769452256 chr14 107349540 4263924 0.03972000252632661 0.23882774666979423 chr15 102531392 2554439 0.024913725934784928 0.17496749375426798 chr16 90354753 2135639 0.02363615558774202 0.21139875891667514 chr17 81195210 2934074 0.03613604792696515 0.23048024667839379 chr18 78077248 3087399 0.03954287681860918 0.6205136068765889 chr19 59128983 2136462 0.0361322297730032 0.5165884966199861 chr20 63025520 1548724 0.02457296663319874 0.19319460813601372 chr21 48129895 2294293 0.04766877218410719 0.26971227324942937 chr22 51304566 1046110 0.020390192950857436 0.16134955984176078 chrMT 16571 489994 29.569368173314828 14.98210421421823 chrX 155270560 8499999 0.05474314641487736 0.29724418102666283 chrY 59373566 337775 0.005688979503100757 0.1457009744618327