BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708653.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 21,223,508 number of mapped reads = 20,717,106 (97.61%) number of supplementary alignments = 519 (0%) number of secondary alignments = 0 number of mapped bases = 1,033,557,837 bp number of sequenced bases = 1,033,461,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,668 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4131 >>>>>>> ACTG content number of A's = 314,518,521 bp (30.43%) number of C's = 200,195,188 bp (19.37%) number of T's = 313,959,491 bp (30.38%) number of G's = 204,751,613 bp (19.81%) number of N's = 36,578 bp (0%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 2,111,590 number of insertions = 64,789 mapped reads with insertion percentage = 0.31% number of deletions = 57,270 mapped reads with deletion percentage = 0.28% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.3339X std coverageData = 0.6745X There is a 24.86% of reference with a coverageData >= 1X There is a 6.34% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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 85541855 0.34319615596865455 0.6921805025414509 chr2 243199373 74675039 0.30705276119276836 0.6345420545747441 chr3 198022430 81373808 0.4109322767122896 0.737370789360679 chr4 191154276 68409498 0.3578758447443781 0.6825436300481453 chr5 180915260 67725657 0.3743501626120428 0.6992630242749246 chr6 171115067 64782852 0.37859233050471236 0.7082523070508088 chr7 159138663 61502489 0.38647106768768064 0.7257378497121706 chr8 146364022 56372600 0.385153395142421 0.7137468617640631 chr9 141213431 48566502 0.3439226825386036 0.6977136608396092 chr10 135534747 49880506 0.3680274402253468 0.694330183770695 chr11 135006516 50543122 0.37437542644238003 0.7219781782785842 chr12 133851895 51243741 0.38283911482911764 0.7177322356011695 chr13 115169878 40649493 0.3529524707840708 0.6927298455602156 chr14 107349540 35079226 0.3267757458485616 0.6725328141253204 chr15 102531392 29732622 0.289985549011175 0.6320952649711199 chr16 90354753 22062287 0.24417406132469865 0.569546924866627 chr17 81195210 15057518 0.18544835341887778 0.49739318261742743 chr18 78077248 42676653 0.5465952514105006 0.8621863167658702 chr19 59128983 8855407 0.14976423660119437 0.4336708151253279 chr20 63025520 17885168 0.28377660350918166 0.6139256143079781 chr21 48129895 13787052 0.2864550608306958 0.6479510078826923 chr22 51304566 6719628 0.13097524302222924 0.41400957893036544 chrMT 16571 1596 0.09631283567678474 0.3208864594581831 chrX 155270560 35753396 0.23026513203790855 0.542456406527764 chrY 59373566 4680122 0.07882501111690007 0.3300954246952525