BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089694.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 19,402,841 number of mapped reads = 15,941,072 (82.16%) number of supplementary alignments = 695 (0%) number of secondary alignments = 0 number of mapped bases = 746,118,337 bp number of sequenced bases = 745,964,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,523,353 duplication rate = 7.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2582 >>>>>>> ACTG content number of A's = 239,211,586 bp (32.07%) number of C's = 147,368,828 bp (19.76%) number of T's = 198,812,749 bp (26.65%) number of G's = 160,501,678 bp (21.52%) number of N's = 69,222 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 3,540,907 number of insertions = 32,524 mapped reads with insertion percentage = 0.2% number of deletions = 102,139 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.241X std coverageData = 1.3181X There is a 13.62% of reference with a coverageData >= 1X There is a 4.98% of reference with a coverageData >= 2X There is a 2.23% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 57315885 0.2299528272790141 1.4951691946116927 chr2 243199373 74341840 0.3056826959829374 1.7638078648253208 chr3 198022430 69040505 0.348649923142545 1.0621352478989416 chr4 191154276 28215198 0.14760432562858286 0.6522396291532884 chr5 180915260 32519206 0.17974827551860467 0.6925929150929656 chr6 171115067 48204587 0.28170860605746656 1.0778065290584904 chr7 159138663 50574469 0.31780126869609304 2.0102732208262943 chr8 146364022 61162381 0.4178785207200715 2.9473290859109307 chr9 141213431 25943714 0.18371987576734114 1.114109481304784 chr10 135534747 31002516 0.22874219848582444 1.181627093229055 chr11 135006516 36767720 0.27234033652123874 1.1465782322627571 chr12 133851895 25415753 0.18987966513286944 0.7430395343831556 chr13 115169878 21816556 0.1894293575617055 0.7166194892795387 chr14 107349540 25243494 0.2351523257575207 0.9076590684755187 chr15 102531392 18685563 0.18224236144184994 0.705209147976751 chr16 90354753 14260544 0.15782837677615033 0.715725539890719 chr17 81195210 17192716 0.21174544656020966 0.847461152362988 chr18 78077248 37027152 0.47423741164647604 1.7423779528160537 chr19 59128983 12108767 0.20478564632170318 1.4817949452401722 chr20 63025520 16466648 0.2612695301839636 0.8923146681146928 chr21 48129895 12176282 0.25298791946252946 0.9571672605909051 chr22 51304566 5849282 0.11401094397718908 0.5458507391790832 chrMT 16571 309032 18.648965059441192 15.331251158623914 chrX 155270560 22825375 0.14700388148274857 0.8716197507940443 chrY 59373566 1653152 0.02784323245802686 0.48841400422492576