BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230386.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 = 2,238,060 number of mapped reads = 1,667,390 (74.5%) number of supplementary alignments = 14,695 (0.66%) number of secondary alignments = 0 number of mapped bases = 110,328,538 bp number of sequenced bases = 110,279,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,410 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1266 >>>>>>> ACTG content number of A's = 30,390,126 bp (27.56%) number of C's = 19,334,111 bp (17.53%) number of T's = 36,503,745 bp (33.1%) number of G's = 23,838,473 bp (21.62%) number of N's = 213,452 bp (0.19%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,145,688 number of insertions = 9,806 mapped reads with insertion percentage = 0.58% number of deletions = 29,312 mapped reads with deletion percentage = 1.74% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.3176X There is a 3.1% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 7676919 0.030799999491275088 0.5329714982434056 chr2 243199373 8515207 0.0350132769462362 0.29193419249767755 chr3 198022430 7311024 0.03692018121381502 0.21211726113486876 chr4 191154276 8226354 0.04303515554106673 0.24172048153977355 chr5 180915260 7602194 0.042020744960928114 0.22913672471588944 chr6 171115067 7511447 0.043897052034582086 0.28214325684310587 chr7 159138663 6129277 0.03851532295454813 0.40768905429061025 chr8 146364022 6243066 0.04265437581375019 0.5403115996531268 chr9 141213431 5374503 0.03805943217964869 0.30377170996018404 chr10 135534747 5338440 0.03938798070726469 0.2871804563571523 chr11 135006516 4253463 0.03150561266242883 0.2586304820323193 chr12 133851895 4853060 0.036256939059398446 0.214581425658932 chr13 115169878 3743854 0.0325072324900787 0.2000591246889351 chr14 107349540 3388872 0.03156857495616656 0.20963841407506154 chr15 102531392 2722772 0.026555496291321198 0.1806890696764955 chr16 90354753 2744422 0.030373853160773956 0.20936338521121312 chr17 81195210 2259677 0.027830176188964842 0.1966971710319957 chr18 78077248 3275636 0.04195378402681406 0.5506441066950201 chr19 59128983 1920207 0.032474886300682695 0.36393784961252956 chr20 63025520 1621704 0.02573091027253722 0.1893733046041991 chr21 48129895 1050876 0.021834163569232803 0.18160384775255647 chr22 51304566 1053608 0.02053633978698894 0.15903358228534717 chrMT 16571 102629 6.193289481624525 3.6698636538009772 chrX 155270560 7133057 0.045939532903082204 0.26330608121994353 chrY 59373566 276270 0.004653080800300928 0.11260871995007421