BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085145.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 = 2,329,337 number of mapped reads = 2,089,646 (89.71%) number of supplementary alignments = 21,067 (0.9%) number of secondary alignments = 0 number of mapped bases = 140,273,711 bp number of sequenced bases = 140,224,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,506 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.069 >>>>>>> ACTG content number of A's = 39,325,037 bp (28.04%) number of C's = 26,000,815 bp (18.54%) number of T's = 43,966,072 bp (31.35%) number of G's = 30,901,530 bp (22.04%) number of N's = 30,975 bp (0.02%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,235,669 number of insertions = 10,943 mapped reads with insertion percentage = 0.52% number of deletions = 30,730 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.0453X std coverageData = 0.3822X There is a 4% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.05% 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 11121691 0.04462051470676175 0.6391780347665537 chr2 243199373 11967306 0.049207799561226666 0.47236049931319707 chr3 198022430 9676134 0.048863828203703996 0.24245556911216198 chr4 191154276 9495745 0.04967581787184295 0.25246947958177024 chr5 180915260 8529859 0.04714836658886597 0.23935492804253952 chr6 171115067 8298453 0.048496331418904214 0.294126085773035 chr7 159138663 7857689 0.049376366822938556 0.5273216768586216 chr8 146364022 7223089 0.04935016748856492 0.6006428022150611 chr9 141213431 5917045 0.04190143216617972 0.35037520242432457 chr10 135534747 6499978 0.0479580192081666 0.34833899622606207 chr11 135006516 6263272 0.0463923682024355 0.33080429366458375 chr12 133851895 6391501 0.047750545481631025 0.24403015239894849 chr13 115169878 4641913 0.0403049224381396 0.22137873085982118 chr14 107349540 4256003 0.03964621553105863 0.23841325144113462 chr15 102531392 3947907 0.038504373372791036 0.22571454066662353 chr16 90354753 3759948 0.041613173354588216 0.24828262151245797 chr17 81195210 3493066 0.04302059197827064 0.253559758895438 chr18 78077248 3759740 0.048154105021734374 0.6222858221116883 chr19 59128983 2524283 0.0426911283084304 0.48940148760429 chr20 63025520 2680196 0.042525567420943135 0.23300459274120816 chr21 48129895 1842269 0.03827702096586747 0.2260252971373041 chr22 51304566 1436483 0.027999125847785165 0.1820946017933895 chrMT 16571 11487 0.6931989620421217 0.9087574491104653 chrX 155270560 8347121 0.053758555388735633 0.28795435949029863 chrY 59373566 331533 0.005583848542969442 0.11664657693361086