BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082908.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 = 1,952,138 number of mapped reads = 1,729,115 (88.58%) number of supplementary alignments = 24,405 (1.25%) number of secondary alignments = 0 number of mapped bases = 114,393,666 bp number of sequenced bases = 114,350,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,762 duplication rate = 5.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8979 >>>>>>> ACTG content number of A's = 31,256,668 bp (27.33%) number of C's = 21,266,197 bp (18.6%) number of T's = 36,202,557 bp (31.66%) number of G's = 25,620,029 bp (22.4%) number of N's = 5,299 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 834,755 number of insertions = 9,353 mapped reads with insertion percentage = 0.54% number of deletions = 26,252 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3012X There is a 2.89% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 11047680 0.04432358064215214 0.4143041605124724 chr2 243199373 11564575 0.04755182900903285 0.4759132148847688 chr3 198022430 8260848 0.041716728756434306 0.25202570448325834 chr4 191154276 6631661 0.03469271595054457 0.23306226959226958 chr5 180915260 5401026 0.029853899554962916 0.21350509766327153 chr6 171115067 8287180 0.04843045177313345 0.30940022037773485 chr7 159138663 6664625 0.04187935775230184 0.29775963234620983 chr8 146364022 9794037 0.06691560443727079 0.3779246746403881 chr9 141213431 3402444 0.024094337032289796 0.25231326876714544 chr10 135534747 3233831 0.02385979294298605 0.21485077590859297 chr11 135006516 5029657 0.0372549203476964 0.268202234388735 chr12 133851895 4038468 0.030171167916599163 0.21835886830631202 chr13 115169878 3036667 0.02636685088786844 0.20411355798869593 chr14 107349540 2829069 0.02635380645319952 0.21076035728800374 chr15 102531392 2447916 0.02387479534072843 0.191598746998256 chr16 90354753 4079437 0.04514911351702771 0.2691763589500063 chr17 81195210 2347041 0.028906150990926683 0.2165926209883217 chr18 78077248 3994384 0.05115938512586919 0.47958237233349027 chr19 59128983 1903495 0.03219224994957211 0.3170445453151996 chr20 63025520 1932680 0.030665038543117137 0.2231439303094654 chr21 48129895 1851663 0.03847220111325819 0.24473028644508815 chr22 51304566 1579116 0.030779248770957345 0.2163866919823224 chrMT 16571 227904 13.753183271981172 9.351271211699558 chrX 155270560 4594500 0.029590284210992735 0.223588106089019 chrY 59373566 213762 0.003600289057928574 0.07474445844050431