BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085034.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 = 2,687,753 number of mapped reads = 2,442,114 (90.86%) number of supplementary alignments = 18,288 (0.68%) number of secondary alignments = 0 number of mapped bases = 163,269,220 bp number of sequenced bases = 163,209,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,177 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1272 >>>>>>> ACTG content number of A's = 45,838,505 bp (28.09%) number of C's = 31,730,472 bp (19.44%) number of T's = 49,688,829 bp (30.44%) number of G's = 35,934,030 bp (22.02%) number of N's = 17,922 bp (0.01%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,423,410 number of insertions = 11,452 mapped reads with insertion percentage = 0.46% number of deletions = 34,633 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.3943X There is a 4.43% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13503828 0.05417771055422967 0.5780376485978034 chr2 243199373 16453556 0.0676545987641177 0.5166726610596556 chr3 198022430 10338991 0.052211211628904866 0.26809175739146995 chr4 191154276 9633509 0.0503965132331123 0.264620132380304 chr5 180915260 7827886 0.04326824613910402 0.23798667121410275 chr6 171115067 11245594 0.06571948453843635 0.38946921789568256 chr7 159138663 14259966 0.0896071748447453 0.46878668512415683 chr8 146364022 10472187 0.0715489152108706 0.6745028802966239 chr9 141213431 4893326 0.034651987175355864 0.3245715206552351 chr10 135534747 11449463 0.08447621922369472 0.5506399785197981 chr11 135006516 7125659 0.05278011173919931 0.38526297370348417 chr12 133851895 6887553 0.05145652215084441 0.26764510862155605 chr13 115169878 3118728 0.027079372264334604 0.18691428082466513 chr14 107349540 5210854 0.04854099980307321 0.26558971342652526 chr15 102531392 2802083 0.027329025241362177 0.1985011718917548 chr16 90354753 4668537 0.05166896975524907 0.27704411716880084 chr17 81195210 2727138 0.03358742467689904 0.2436887995925342 chr18 78077248 3711668 0.047538407091397485 0.5223140088057421 chr19 59128983 2503520 0.04233998071639419 0.4230694140123267 chr20 63025520 3779506 0.05996786698467541 0.28439204127291 chr21 48129895 1838085 0.038190089548294254 0.23434351252373364 chr22 51304566 1225937 0.02389528058769662 0.17582978810168653 chrMT 16571 11808 0.7125701526763624 0.9738369477006259 chrX 155270560 7261209 0.04676487931775347 0.27520146233551407 chrY 59373566 318629 0.0053665127676515165 0.10993820342537922