BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081963.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 = 2,904,656 number of mapped reads = 2,638,643 (90.84%) number of supplementary alignments = 19,785 (0.68%) number of secondary alignments = 0 number of mapped bases = 176,867,693 bp number of sequenced bases = 176,804,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,639 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9637 >>>>>>> ACTG content number of A's = 48,825,138 bp (27.62%) number of C's = 32,725,477 bp (18.51%) number of T's = 55,768,556 bp (31.54%) number of G's = 39,463,429 bp (22.32%) number of N's = 22,281 bp (0.01%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,338,835 number of insertions = 12,293 mapped reads with insertion percentage = 0.46% number of deletions = 35,337 mapped reads with deletion percentage = 1.32% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.4524X There is a 4.74% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.13% 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 16669877 0.06687998181557188 0.773659780564426 chr2 243199373 15552145 0.06394812950442927 0.6130376977029278 chr3 198022430 11143047 0.05627164054092256 0.2745241570544725 chr4 191154276 8840546 0.04624822517702926 0.26602376058079646 chr5 180915260 8977416 0.049622215395207676 0.2588722982342774 chr6 171115067 14016530 0.08191289198396538 0.42337972449030065 chr7 159138663 11817104 0.07425665000088634 0.5809230647769489 chr8 146364022 9814593 0.06705604878772735 0.6140283518927299 chr9 141213431 8688284 0.06152590400554746 0.4769306699556944 chr10 135534747 7075496 0.05220429562612457 0.43285385269651044 chr11 135006516 8149301 0.060362279106587716 0.36813347377062267 chr12 133851895 7581791 0.05664313531011272 0.2849388871212376 chr13 115169878 4764818 0.04137208515580784 0.2378619231395938 chr14 107349540 4574134 0.042609721476216854 0.26836247054730794 chr15 102531392 4124801 0.04022964010866058 0.23637821276557458 chr16 90354753 3978532 0.0440323488018389 0.27334835409000285 chr17 81195210 5057020 0.062282245467435826 0.3275288200006438 chr18 78077248 4842602 0.062023215777277395 0.7175253780316927 chr19 59128983 3950953 0.06681922805944422 0.5974044441956181 chr20 63025520 4719331 0.07487968365830222 0.32339329486172647 chr21 48129895 1885864 0.03918279896517539 0.2576322972245305 chr22 51304566 1563546 0.030475767010678934 0.2003374405233585 chrMT 16571 20041 1.2094019672922576 1.2254417323347866 chrX 155270560 8658424 0.055763462178535325 0.31815701145330677 chrY 59373566 401497 0.006762218055085322 0.14599513960482421