BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472469.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 28,725,020 number of mapped reads = 28,416,494 (98.93%) number of supplementary alignments = 41,177 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,297,539 number of mapped paired reads (second in pair) = 14,118,955 number of mapped paired reads (both in pair) = 28,193,678 number of mapped paired reads (singletons) = 222,816 number of mapped bases = 2,803,657,074 bp number of sequenced bases = 2,803,251,300 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,487,972 duplication rate = 50.72% >>>>>>> Insert size mean insert size = 47,996.2024 std insert size = 2,190,993.1268 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 54.8575 >>>>>>> ACTG content number of A's = 786,842,251 bp (28.07%) number of C's = 613,741,544 bp (21.89%) number of T's = 793,072,523 bp (28.29%) number of G's = 609,222,511 bp (21.73%) number of N's = 372,471 bp (0.01%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 14,192,745 number of insertions = 138,157 mapped reads with insertion percentage = 0.48% number of deletions = 170,189 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.9057X std coverageData = 17.3484X There is a 7.65% of reference with a coverageData >= 1X There is a 2.93% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.6% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.55% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.53% of reference with a coverageData >= 15X There is a 0.52% of reference with a coverageData >= 16X There is a 0.51% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.49% of reference with a coverageData >= 19X There is a 0.49% of reference with a coverageData >= 20X There is a 0.48% of reference with a coverageData >= 21X There is a 0.47% of reference with a coverageData >= 22X There is a 0.47% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.45% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.44% of reference with a coverageData >= 28X There is a 0.43% of reference with a coverageData >= 29X There is a 0.43% of reference with a coverageData >= 30X There is a 0.42% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.41% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.4% of reference with a coverageData >= 36X There is a 0.39% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.39% of reference with a coverageData >= 39X There is a 0.38% of reference with a coverageData >= 40X There is a 0.38% of reference with a coverageData >= 41X There is a 0.37% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.36% of reference with a coverageData >= 45X There is a 0.36% of reference with a coverageData >= 46X There is a 0.36% of reference with a coverageData >= 47X There is a 0.35% of reference with a coverageData >= 48X There is a 0.35% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 304477183 1.2215704088456414 20.815343516614412 chr2 243199373 209636888 0.8619960052281879 17.817776595487665 chr3 198022430 246227568 1.2434327161827072 19.145068604137062 chr4 191154276 101863674 0.5328872371131264 13.200139336397578 chr5 180915260 133232035 0.7364333721765649 15.217301479474344 chr6 171115067 197080459 1.1517422892982299 18.18672470078644 chr7 159138663 166509641 1.0463179585717646 20.429509361655956 chr8 146364022 165579855 1.1312879540847818 19.453356547345052 chr9 141213431 130892366 0.9269115910086485 15.421536091898176 chr10 135534747 73972663 0.5457837538885877 11.96584928217916 chr11 135006516 109590062 0.8117390570985478 16.767131034895137 chr12 133851895 124313517 0.9287393129548147 14.966312350231842 chr13 115169878 79463480 0.6899675625253332 17.773934888868215 chr14 107349540 74860446 0.6973522755663415 14.340090871469686 chr15 102531392 69876131 0.681509629753198 15.947417617845508 chr16 90354753 140675889 1.556928488310958 27.313132868664443 chr17 81195210 144159772 1.775471385565725 26.51680930339944 chr18 78077248 44396696 0.5686252671200707 11.448900292538188 chr19 59128983 70944953 1.199833810772629 15.881180775791558 chr20 63025520 59245740 0.9400277855700357 17.549508676800805 chr21 48129895 23663562 0.49166037033739635 19.050164817404802 chr22 51304566 45105794 0.8791769917710638 18.092416946388095 chrMT 16571 59593 3.596222316094382 2.3816642798154013 chrX 155270560 82298872 0.5300352623188839 8.33907953263684 chrY 59373566 5530235 0.09314304955171465 2.6573481070209892