BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472724.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 = 18,571,332 number of mapped reads = 18,411,607 (99.14%) number of supplementary alignments = 64,556 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,233,873 number of mapped paired reads (second in pair) = 9,177,734 number of mapped paired reads (both in pair) = 18,319,678 number of mapped paired reads (singletons) = 91,929 number of mapped bases = 1,811,488,687 bp number of sequenced bases = 1,811,222,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,769,401 duplication rate = 46.69% >>>>>>> Insert size mean insert size = 23,667.9191 std insert size = 1,480,267.424 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.1464 >>>>>>> ACTG content number of A's = 490,775,011 bp (27.1%) number of C's = 417,501,394 bp (23.05%) number of T's = 487,724,240 bp (26.93%) number of G's = 414,870,748 bp (22.91%) number of N's = 351,354 bp (0.02%) GC percentage = 45.96% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 10,834,621 number of insertions = 101,194 mapped reads with insertion percentage = 0.54% number of deletions = 96,724 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.5852X std coverageData = 21.3969X There is a 5.35% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 202663689 0.8130920123163906 32.85660472988667 chr2 243199373 112852893 0.4640344734770348 15.122972674727897 chr3 198022430 190985265 0.964462788382104 25.122152180339864 chr4 191154276 59297727 0.3102087394581746 9.949587197082444 chr5 180915260 101173347 0.5592305867398913 17.71122325828211 chr6 171115067 118037027 0.6898108335486319 22.717957388640947 chr7 159138663 83504731 0.5247293739045678 23.55144540526239 chr8 146364022 74925404 0.5119113493615255 16.349693632623783 chr9 141213431 142751849 1.0108942753469392 36.488766273540186 chr10 135534747 46419667 0.34249274099430754 11.973852157379488 chr11 135006516 82677060 0.6123931084926301 18.322336984905895 chr12 133851895 75763835 0.56602736180911 16.819125095480118 chr13 115169878 38700316 0.336028106237987 14.62207184554419 chr14 107349540 47324286 0.44084293234978 27.03156084651166 chr15 102531392 44070398 0.4298234632374834 15.419762092585815 chr16 90354753 58864013 0.6514766633250605 17.79409851962299 chr17 81195210 56848668 0.7001480506054483 14.950730192619128 chr18 78077248 46671076 0.5977551360416802 31.104893407978366 chr19 59128983 46181513 0.7810300576284223 20.83130943867593 chr20 63025520 29939708 0.4750410309982369 13.944482565406823 chr21 48129895 13996592 0.2908086959258897 12.669406645160487 chr22 51304566 28476734 0.5550526243609585 15.897294103850536 chrMT 16571 2454 0.14809003681129684 0.5182440102138839 chrX 155270560 104238209 0.6713327304287432 22.13532815176779 chrY 59373566 5122226 0.08627115305824817 4.178363602596704