BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514715.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 40,663,090 number of mapped reads = 40,358,864 (99.25%) number of supplementary alignments = 2,579,057 (6.34%) number of secondary alignments = 0 number of mapped bases = 3,833,196,119 bp number of sequenced bases = 3,829,219,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,742,532 duplication rate = 33.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9435 >>>>>>> ACTG content number of A's = 1,058,912,615 bp (27.65%) number of C's = 847,593,205 bp (22.13%) number of T's = 1,058,962,889 bp (27.65%) number of G's = 858,069,992 bp (22.41%) number of N's = 5,680,917 bp (0.15%) GC percentage = 44.54% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 27,074,901 number of insertions = 1,486,422 mapped reads with insertion percentage = 3.47% number of deletions = 1,681,886 mapped reads with deletion percentage = 3.86% homopolymer indels = 30.53% >>>>>>> Coverage mean coverageData = 1.2382X std coverageData = 142.9043X There is a 7.03% of reference with a coverageData >= 1X There is a 4.72% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 3.34% of reference with a coverageData >= 4X There is a 2.99% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 2.5% of reference with a coverageData >= 7X There is a 2.32% of reference with a coverageData >= 8X There is a 2.16% of reference with a coverageData >= 9X There is a 2.03% of reference with a coverageData >= 10X There is a 1.9% of reference with a coverageData >= 11X There is a 1.8% of reference with a coverageData >= 12X There is a 1.7% of reference with a coverageData >= 13X There is a 1.61% of reference with a coverageData >= 14X There is a 1.53% of reference with a coverageData >= 15X There is a 1.46% of reference with a coverageData >= 16X There is a 1.39% of reference with a coverageData >= 17X There is a 1.33% of reference with a coverageData >= 18X There is a 1.27% of reference with a coverageData >= 19X There is a 1.22% of reference with a coverageData >= 20X There is a 1.17% of reference with a coverageData >= 21X There is a 1.12% of reference with a coverageData >= 22X There is a 1.08% of reference with a coverageData >= 23X There is a 1.04% of reference with a coverageData >= 24X There is a 1% of reference with a coverageData >= 25X There is a 0.96% of reference with a coverageData >= 26X There is a 0.93% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.87% of reference with a coverageData >= 29X There is a 0.84% of reference with a coverageData >= 30X There is a 0.81% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.76% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.7% of reference with a coverageData >= 36X There is a 0.68% of reference with a coverageData >= 37X There is a 0.66% of reference with a coverageData >= 38X There is a 0.64% of reference with a coverageData >= 39X There is a 0.62% of reference with a coverageData >= 40X There is a 0.61% of reference with a coverageData >= 41X There is a 0.59% of reference with a coverageData >= 42X There is a 0.57% of reference with a coverageData >= 43X There is a 0.56% of reference with a coverageData >= 44X There is a 0.54% of reference with a coverageData >= 45X There is a 0.53% of reference with a coverageData >= 46X There is a 0.52% of reference with a coverageData >= 47X There is a 0.5% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.48% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 474340331 1.9030657941670686 265.168024631339 chr2 243199373 180371060 0.7416592311691528 14.46467438128787 chr3 198022430 380710824 1.9225641458899378 408.9234831766604 chr4 191154276 192545086 1.0072758508420707 14.24469439248429 chr5 180915260 229220015 1.2670021036368075 13.021822261549623 chr6 171115067 258892164 1.5129711751215924 12.414624117396613 chr7 159138663 208666820 1.311226423964615 11.879709683181638 chr8 146364022 241362052 1.649053153240077 33.09442564929717 chr9 141213431 96914645 0.686299060320969 14.099547823881325 chr10 135534747 119993856 0.8853364812788561 74.01220667800158 chr11 135006516 198196455 1.468051030959128 15.851896550636873 chr12 133851895 159689064 1.1930280404323002 14.357108799493899 chr13 115169878 130420906 1.132422020973227 96.21814070213493 chr14 107349540 109983579 1.0245370310855548 11.488824113488548 chr15 102531392 82199750 0.8017032481135143 9.59763247850136 chr16 90354753 112186025 1.2416173059540099 21.99744665771334 chr17 81195210 169909317 2.0926027163425034 23.957733604322495 chr18 78077248 49281412 0.631187871785645 10.014883633128477 chr19 59128983 190800073 3.2268451666080575 415.0669034194575 chr20 63025520 33760807 0.5356688370044388 8.212526184053441 chr21 48129895 50554034 1.0503665964781348 18.061582506838796 chr22 51304566 34551362 0.6734558869477622 9.765375825130917 chrMT 16571 1859418 112.20916058173918 62.793057603955965 chrX 155270560 115729272 0.745339438461483 9.680357005491755 chrY 59373566 11057792 0.18624099485619577 7.641080053681983