BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068067.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 = 1,794,165 number of mapped reads = 1,332,373 (74.26%) number of supplementary alignments = 12,630 (0.7%) number of secondary alignments = 0 number of mapped bases = 80,398,572 bp number of sequenced bases = 80,363,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 279,478 duplication rate = 16.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.76 >>>>>>> ACTG content number of A's = 20,007,804 bp (24.9%) number of C's = 13,540,631 bp (16.85%) number of T's = 27,780,462 bp (34.57%) number of G's = 19,027,711 bp (23.68%) number of N's = 7,228 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 561,345 number of insertions = 5,512 mapped reads with insertion percentage = 0.41% number of deletions = 20,924 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.5319X There is a 1.58% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7538375 0.030244157345549805 0.5143781393452391 chr2 243199373 7581785 0.03117518316957174 1.3347978014889403 chr3 198022430 5104750 0.025778645378707856 0.2577178207346392 chr4 191154276 5122371 0.026797051612907682 0.262164562903375 chr5 180915260 4637936 0.025635957961755135 0.2573626412757256 chr6 171115067 4634884 0.027086358210641964 0.49926198005673367 chr7 159138663 4177406 0.026250101146067815 0.37791267276534984 chr8 146364022 3624630 0.024764487545989956 0.3690512162075312 chr9 141213431 3297012 0.023347722498152458 0.2832046507445766 chr10 135534747 3993364 0.02946376548000639 0.3146254158763328 chr11 135006516 3373703 0.024989186447860044 0.27227086576248577 chr12 133851895 3687330 0.02754783561338448 0.2596392588430887 chr13 115169878 2565131 0.02227258589264113 0.3266055995257481 chr14 107349540 2483663 0.02313622396518886 0.24606902496214902 chr15 102531392 2400421 0.02341157135562931 0.30002779636860166 chr16 90354753 2264140 0.025058338657624354 0.2632703690830636 chr17 81195210 1994477 0.024563973662978394 0.2497740804353024 chr18 78077248 2275651 0.02914614767159826 1.142104244723101 chr19 59128983 1592846 0.026938498164258973 0.3940132642574925 chr20 63025520 1658891 0.026320941104492276 0.2525039817255648 chr21 48129895 1238896 0.025740675312090334 0.25495851361754884 chr22 51304566 920326 0.017938481342966626 0.2049517006450679 chrMT 16571 700552 42.27578299438779 23.55957814278503 chrX 155270560 2801222 0.018040908720880506 0.21294494660596924 chrY 59373566 728810 0.012274991197261085 0.2449270580625257