BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230399.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 = 377,856 number of mapped reads = 348,944 (92.35%) number of supplementary alignments = 1,833 (0.49%) number of secondary alignments = 0 number of mapped bases = 24,760,529 bp number of sequenced bases = 24,746,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,893 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7534 >>>>>>> ACTG content number of A's = 7,323,455 bp (29.59%) number of C's = 4,988,584 bp (20.16%) number of T's = 7,372,084 bp (29.79%) number of G's = 5,047,216 bp (20.4%) number of N's = 14,881 bp (0.06%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 236,825 number of insertions = 1,943 mapped reads with insertion percentage = 0.55% number of deletions = 8,440 mapped reads with deletion percentage = 2.39% homopolymer indels = 49.06% >>>>>>> Coverage mean coverageData = 0.008X std coverageData = 0.1247X There is a 0.62% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 2085851 0.008368488678710253 0.16800865756283076 chr2 243199373 3462059 0.014235476667943548 0.16429853963347876 chr3 198022430 1858045 0.009383002723479356 0.11908735286482873 chr4 191154276 1567884 0.008202191616158249 0.11394943016308337 chr5 180915260 852781 0.004713704084442628 0.08553357155025833 chr6 171115067 768740 0.00449253250153594 0.08301949491894069 chr7 159138663 1359862 0.008545139027591303 0.14799681868263037 chr8 146364022 1508879 0.010309084017928941 0.14642944279686881 chr9 141213431 828697 0.005868400718908954 0.10531020637770373 chr10 135534747 1062241 0.007837407185332334 0.12582316385619421 chr11 135006516 1035493 0.007669948315679815 0.12512959541899402 chr12 133851895 1481746 0.01107004125716711 0.13298501525329448 chr13 115169878 368625 0.0032007066986734153 0.06970322121332141 chr14 107349540 816429 0.00760533300841345 0.10981083942345225 chr15 102531392 793239 0.007736547651669452 0.10923678254854172 chr16 90354753 954000 0.010558382025569812 0.12748655379197377 chr17 81195210 403908 0.00497452990145601 0.0950708859551249 chr18 78077248 492754 0.006311108711208674 0.13930507085687227 chr19 59128983 383319 0.006482759901349901 0.12111425928659712 chr20 63025520 669185 0.010617683122646191 0.12716567823237665 chr21 48129895 532711 0.011068193687104448 0.1329800129451155 chr22 51304566 173908 0.003389717788471303 0.07163474095694605 chrMT 16571 1614 0.09739907066562066 0.32877062907512605 chrX 155270560 1242523 0.008002309001783725 0.11295629030526488 chrY 59373566 56036 9.437870044726639E-4 0.038850070387898235