BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472761.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 = 15,063,472 number of mapped reads = 14,914,653 (99.01%) number of supplementary alignments = 55,020 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,488,744 number of mapped paired reads (second in pair) = 7,425,909 number of mapped paired reads (both in pair) = 14,819,472 number of mapped paired reads (singletons) = 95,181 number of mapped bases = 1,467,481,855 bp number of sequenced bases = 1,467,299,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,162,064 duplication rate = 43.18% >>>>>>> Insert size mean insert size = 28,948.492 std insert size = 1,729,919.5009 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 52.8002 >>>>>>> ACTG content number of A's = 409,351,566 bp (27.9%) number of C's = 325,731,489 bp (22.2%) number of T's = 406,995,043 bp (27.74%) number of G's = 324,938,248 bp (22.15%) number of N's = 283,094 bp (0.02%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,249,579 number of insertions = 94,006 mapped reads with insertion percentage = 0.61% number of deletions = 74,848 mapped reads with deletion percentage = 0.5% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.474X std coverageData = 34.0417X There is a 3.66% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 73931704 0.29661592698699835 20.845126455891755 chr2 243199373 272049827 1.1186288173530776 65.16933100157554 chr3 198022430 104010389 0.525245493654431 25.83367289185359 chr4 191154276 33686782 0.17622824194631148 14.81757191849761 chr5 180915260 60710695 0.3355753129946031 25.89088026650181 chr6 171115067 68952811 0.40296165737409906 16.374440844771396 chr7 159138663 175655792 1.1037907990970115 61.84625420381188 chr8 146364022 56585947 0.38661104161239845 29.12111270226078 chr9 141213431 64016104 0.453328720552084 20.560265339864056 chr10 135534747 9832105 0.07254305790676689 8.684149480763073 chr11 135006516 94638000 0.7009883878493687 33.98606756178122 chr12 133851895 152476434 1.1391428862475201 53.129336418541016 chr13 115169878 2138323 0.01856668633442505 0.5854698936357923 chr14 107349540 1925873 0.017940207289197513 1.0470363001311784 chr15 102531392 3696491 0.036052285333256766 2.3544896591673736 chr16 90354753 8257401 0.0913886732665851 6.223805481809515 chr17 81195210 49908516 0.6146731562120474 32.20950768937298 chr18 78077248 53066086 0.6796613272025162 42.63403558653181 chr19 59128983 25368868 0.4290428604192296 22.011565883373702 chr20 63025520 76802493 1.218593563369251 61.1840269423533 chr21 48129895 1739753 0.0361470350184641 1.5329129009535447 chr22 51304566 1510902 0.02944965950983778 1.245820023408743 chrMT 16571 1844 0.11127873996741296 0.38909785374943134 chrX 155270560 76253369 0.4910999805758413 41.91848353652093 chrY 59373566 265346 0.004469093198815109 0.2898386370913803