BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,756,628 number of mapped reads = 1,422,471 (80.98%) number of supplementary alignments = 7,772 (0.44%) number of secondary alignments = 0 number of mapped bases = 87,395,333 bp number of sequenced bases = 87,365,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,941 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4644 >>>>>>> ACTG content number of A's = 26,392,719 bp (30.21%) number of C's = 17,037,039 bp (19.5%) number of T's = 25,221,148 bp (28.87%) number of G's = 18,713,016 bp (21.42%) number of N's = 1,958 bp (0%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 777,485 number of insertions = 6,918 mapped reads with insertion percentage = 0.48% number of deletions = 18,327 mapped reads with deletion percentage = 1.28% homopolymer indels = 44.9% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2401X There is a 2.58% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 7182026 0.02881447585239918 0.36784689910939766 chr2 243199373 7372600 0.030315045261239223 0.2456160082519456 chr3 198022430 5695609 0.028762443729228048 0.18173932086209804 chr4 191154276 5820505 0.03044925346059222 0.1945317987730685 chr5 180915260 5064529 0.027993929312541133 0.17826274960630328 chr6 171115067 5091136 0.02975270436004329 0.20878117602966467 chr7 159138663 5037071 0.03165208821692815 0.24286775966188567 chr8 146364022 4262940 0.029125600279008457 0.39222245371826986 chr9 141213431 3693524 0.026155614050621008 0.22004901381382685 chr10 135534747 3842034 0.02834722523221296 0.25388647590561486 chr11 135006516 3998057 0.02961380767725315 0.22719546874033686 chr12 133851895 4104807 0.030666782864747638 0.18772528381799003 chr13 115169878 2962247 0.025720674984130835 0.17030487056812205 chr14 107349540 2689740 0.025055906154791162 0.17794920705713813 chr15 102531392 2618443 0.025537964021789542 0.1696585967059113 chr16 90354753 2468927 0.027324815995014674 0.19103735216208614 chr17 81195210 2063826 0.025418075770725884 0.18089770220998194 chr18 78077248 2262709 0.028980388755505317 0.3832991197118322 chr19 59128983 1502846 0.025416401969910424 0.2639553323709689 chr20 63025520 1744840 0.027684658531972446 0.1813339796181715 chr21 48129895 1185064 0.02462220206381086 0.17813680740688068 chr22 51304566 948545 0.01848851035987713 0.14457592772378589 chrMT 16571 6301 0.38024259248084 0.6759135410902465 chrX 155270560 5534948 0.0356471181658648 0.2182605415094616 chrY 59373566 242059 0.004076881621023066 0.0903659159695036