BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237317.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,571,821 number of mapped reads = 2,233,493 (86.84%) number of supplementary alignments = 18,976 (0.74%) number of secondary alignments = 0 number of mapped bases = 148,880,398 bp number of sequenced bases = 148,819,131 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,927 duplication rate = 4.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4358 >>>>>>> ACTG content number of A's = 41,395,144 bp (27.82%) number of C's = 27,188,013 bp (18.27%) number of T's = 47,269,734 bp (31.76%) number of G's = 32,963,976 bp (22.15%) number of N's = 2,264 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,182,711 number of insertions = 11,009 mapped reads with insertion percentage = 0.49% number of deletions = 35,416 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.4766X There is a 3.73% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14076496 0.05647526952400251 0.7590523876401114 chr2 243199373 9813347 0.040351037418176236 0.503740187380528 chr3 198022430 10059798 0.05080130569047153 0.27794502643074337 chr4 191154276 12018091 0.06287115962815291 0.348989625613148 chr5 180915260 6792481 0.037545097080257356 0.24351556812799138 chr6 171115067 7748806 0.045284182952749566 0.31026206948557195 chr7 159138663 6916368 0.04346126748595343 0.4157183803646652 chr8 146364022 7584054 0.05181638148752157 1.094610284432775 chr9 141213431 6843743 0.04846382494594299 0.46351965805213585 chr10 135534747 8738703 0.06447573919918853 0.4689868239378873 chr11 135006516 5247835 0.038870975679425726 0.333139121580564 chr12 133851895 7990997 0.059700290384383424 0.3187606362166063 chr13 115169878 6351345 0.0551476228879916 0.2897309491029421 chr14 107349540 3923183 0.036545876209623254 0.2910426928089514 chr15 102531392 4763362 0.04645759612821798 0.2714417279375833 chr16 90354753 3522189 0.03898177885561814 0.2778584916768487 chr17 81195210 3848885 0.04740285787794625 0.29361681958904 chr18 78077248 3987097 0.05106605447978904 0.8128699152965869 chr19 59128983 2687243 0.045447137150997505 0.5109598036279585 chr20 63025520 2987433 0.04740037051657805 0.2877804832739635 chr21 48129895 1753468 0.03643199304714876 0.2790327650834653 chr22 51304566 1449612 0.028255028996834318 0.20299193455068623 chrMT 16571 19231 1.1605213927946412 1.5086422194388107 chrX 155270560 9310674 0.05996419411381011 0.34155012735589385 chrY 59373566 445957 0.007511036140224423 0.24790281885067753