BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818925.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 796,637 number of mapped reads = 784,011 (98.42%) number of supplementary alignments = 10,911 (1.37%) number of secondary alignments = 0 number of mapped bases = 72,643,297 bp number of sequenced bases = 72,602,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 202,008 duplication rate = 23.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9986 >>>>>>> ACTG content number of A's = 21,158,715 bp (29.14%) number of C's = 14,759,026 bp (20.33%) number of T's = 20,706,642 bp (28.52%) number of G's = 15,975,638 bp (22%) number of N's = 2,956 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 449,443 number of insertions = 9,431 mapped reads with insertion percentage = 1.18% number of deletions = 22,101 mapped reads with deletion percentage = 2.76% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2834X There is a 1.57% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 8270418 0.03318113297699667 0.45028791108983224 chr2 243199373 6473968 0.02662000284022114 0.38228269634967477 chr3 198022430 4927118 0.024881615683637455 0.2171339845240915 chr4 191154276 4755392 0.0248772462720112 0.23123714322607042 chr5 180915260 3848523 0.02127251731003786 0.20396915665756932 chr6 171115067 4035421 0.023583084007441614 0.2218205025540216 chr7 159138663 3709722 0.02331125529187084 0.24594334559529724 chr8 146364022 4861648 0.03321614105411779 0.27304804212548806 chr9 141213431 2812026 0.019913304138895967 0.29187323924163394 chr10 135534747 3284348 0.024232516551641183 0.31350426210398225 chr11 135006516 2757013 0.020421332848853013 0.22009618275393147 chr12 133851895 3316276 0.024775711991227318 0.22129096407354615 chr13 115169878 1175699 0.01020838973190542 0.13950972933344188 chr14 107349540 1420758 0.013234877392115513 0.17225750361008024 chr15 102531392 2136128 0.020833892511670962 0.19972983012791926 chr16 90354753 2197363 0.024319285118293666 0.30489789680979656 chr17 81195210 1489873 0.018349272081444212 0.19861219060337643 chr18 78077248 1759899 0.022540484521175748 0.3633060561955846 chr19 59128983 1117925 0.018906548756301118 0.3779126834975485 chr20 63025520 1614351 0.025614243246227877 0.23309113484792235 chr21 48129895 956268 0.01986848298754859 0.20775527189223444 chr22 51304566 872016 0.01699684975407452 0.18707501856778583 chrMT 16571 313076 18.89300585359966 12.309982060793294 chrX 155270560 4317313 0.02780509711564124 0.2536640855668709 chrY 59373566 220755 0.003718068744599238 0.20177245860673812