BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472477.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 = 17,652,046 number of mapped reads = 17,456,531 (98.89%) number of supplementary alignments = 72,561 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,757,599 number of mapped paired reads (second in pair) = 8,698,932 number of mapped paired reads (both in pair) = 17,348,026 number of mapped paired reads (singletons) = 108,505 number of mapped bases = 1,717,011,067 bp number of sequenced bases = 1,716,774,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,061,964 duplication rate = 45.74% >>>>>>> Insert size mean insert size = 33,969.2428 std insert size = 1,815,126.2864 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.1019 >>>>>>> ACTG content number of A's = 482,254,864 bp (28.09%) number of C's = 378,532,684 bp (22.05%) number of T's = 479,686,892 bp (27.94%) number of G's = 376,031,702 bp (21.9%) number of N's = 267,994 bp (0.02%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,518,399 number of insertions = 95,411 mapped reads with insertion percentage = 0.54% number of deletions = 92,090 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.44% >>>>>>> Coverage mean coverageData = 0.5546X std coverageData = 19.0938X There is a 5.76% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 145431916 0.5834766445777481 18.862858362996512 chr2 243199373 145015271 0.5962814344920206 22.5823215340359 chr3 198022430 186288069 0.9407422633890514 23.79808367915298 chr4 191154276 67932282 0.35537934814495076 13.34681698418373 chr5 180915260 99459263 0.5497560736446444 18.827999451083805 chr6 171115067 124175434 0.7256838113501718 22.308971902930022 chr7 159138663 69710597 0.4380494072644056 13.834140861578401 chr8 146364022 72859685 0.4977977784731824 20.66964743998106 chr9 141213431 110771426 0.7844255692647253 23.313874003370394 chr10 135534747 55341496 0.40831961710896175 13.95295423007119 chr11 135006516 93311868 0.6911656619596049 27.75691588743903 chr12 133851895 80377378 0.6004948827956451 18.3933991345072 chr13 115169878 37906501 0.32913554879340934 13.21325015916175 chr14 107349540 39463174 0.36761381557852973 11.314621573360684 chr15 102531392 54066892 0.5273203742323131 17.48971941898953 chr16 90354753 55748597 0.6169968391148167 16.857409939515293 chr17 81195210 74650726 0.9193981516889974 30.424217061419792 chr18 78077248 30222261 0.3870815349434447 18.025814909939335 chr19 59128983 28654091 0.4846031429290776 13.068260954963723 chr20 63025520 46944116 0.74484297789213 22.187842851034933 chr21 48129895 7097099 0.14745718851038425 4.23852048068964 chr22 51304566 13717054 0.26736516979794744 8.024503325886846 chrMT 16571 2886 0.17415967654335887 0.6020991568631392 chrX 155270560 74991342 0.482972058579553 15.650252333253942 chrY 59373566 2871643 0.04836568179179267 1.4031600267186521