BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085136.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 = 1,736,489 number of mapped reads = 1,533,055 (88.28%) number of supplementary alignments = 25,006 (1.44%) number of secondary alignments = 0 number of mapped bases = 102,055,777 bp number of sequenced bases = 102,020,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,172 duplication rate = 2.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0224 >>>>>>> ACTG content number of A's = 29,238,259 bp (28.66%) number of C's = 19,431,959 bp (19.05%) number of T's = 30,586,839 bp (29.98%) number of G's = 22,745,090 bp (22.29%) number of N's = 18,119 bp (0.02%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 925,415 number of insertions = 9,260 mapped reads with insertion percentage = 0.6% number of deletions = 21,552 mapped reads with deletion percentage = 1.39% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.4473X There is a 3.01% of reference with a coverageData >= 1X There is a 0.16% 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 0.01% 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 8163134 0.03275070676754703 0.8914445206349904 chr2 243199373 8733422 0.03591054488450511 0.4619859754066144 chr3 198022430 6811970 0.03439999196050669 0.19623517327553464 chr4 191154276 6645309 0.03476411377792041 0.21029632027611783 chr5 180915260 6227606 0.034422778929759715 0.19893983133729143 chr6 171115067 5956037 0.034807203739691726 0.2764123638046513 chr7 159138663 5652425 0.03551886696446608 0.40985536148024454 chr8 146364022 5365651 0.03665963073903503 0.8994353255385719 chr9 141213431 4319113 0.030585709655337245 0.4007021313353191 chr10 135534747 4769076 0.035187109619941224 0.3689727697669004 chr11 135006516 4682650 0.03468462218519883 0.4594068005849242 chr12 133851895 4576661 0.03419197763318928 0.20464809201318238 chr13 115169878 3187438 0.02767596923216329 0.173795863022574 chr14 107349540 3062890 0.028531934091194058 0.22092225346461264 chr15 102531392 2835603 0.027655949506664262 0.1796407550189956 chr16 90354753 2719178 0.030094465534093152 0.23248858023569383 chr17 81195210 2639509 0.03250818613561071 0.2616699525647919 chr18 78077248 2788994 0.03572095676323018 0.8235132276751364 chr19 59128983 2012549 0.03403659082044418 0.5578723383552764 chr20 63025520 1995987 0.03166950467048903 0.2034973084133811 chr21 48129895 1323643 0.027501472837204402 0.2018158025218127 chr22 51304566 1060617 0.020672955307720564 0.15017472555211922 chrMT 16571 35134 2.1202100054311748 1.8078304504960268 chrX 155270560 6192655 0.03988299520527266 0.27559010528557926 chrY 59373566 298526 0.0050279277481834255 0.13414609050266305