BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524861.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,674,686 number of mapped reads = 1,533,000 (91.54%) number of supplementary alignments = 7,721 (0.46%) number of secondary alignments = 0 number of mapped bases = 89,452,211 bp number of sequenced bases = 89,426,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,012 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6455 >>>>>>> ACTG content number of A's = 23,346,637 bp (26.11%) number of C's = 17,234,857 bp (19.27%) number of T's = 28,005,272 bp (31.32%) number of G's = 20,827,886 bp (23.29%) number of N's = 11,476 bp (0.01%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 432,134 number of insertions = 5,858 mapped reads with insertion percentage = 0.38% number of deletions = 16,658 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2845X There is a 2.64% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 7537253 0.030239655852251617 0.5652815907265769 chr2 243199373 5836389 0.023998371903697302 0.29885715459772294 chr3 198022430 6406999 0.03235491555173826 0.19141172979391538 chr4 191154276 4761475 0.024909068735663543 0.18210775946064994 chr5 180915260 5361591 0.02963592457595893 0.18429454592209207 chr6 171115067 5843868 0.0341516857776177 0.21777482770131212 chr7 159138663 4101139 0.025770852429494145 0.37600411654921323 chr8 146364022 9757604 0.06666668397510968 0.37215157420900385 chr9 141213431 3689097 0.02612426434139965 0.23393984324838266 chr10 135534747 4448937 0.03282506588513424 0.26851671077640477 chr11 135006516 4333892 0.032101354278337206 0.24703476400683594 chr12 133851895 3546317 0.02649433539958474 0.1796200891696903 chr13 115169878 2311844 0.02007333896802426 0.15072592592796674 chr14 107349540 1566122 0.014588995909996447 0.13933828502318327 chr15 102531392 2684606 0.026183259074450096 0.17366797035368683 chr16 90354753 2640497 0.029223664636657244 0.19400628757985033 chr17 81195210 2585824 0.0318470018120527 0.21451612769864042 chr18 78077248 2133763 0.027328870505271906 0.392990587650523 chr19 59128983 1417447 0.02397211871545296 0.39739621478267556 chr20 63025520 1941118 0.030798920818106697 0.18906128805203648 chr21 48129895 1279656 0.026587550211775862 0.186335335443052 chr22 51304566 575518 0.011217676025170938 0.11140780768483238 chrMT 16571 16517 0.9967412950334923 1.1686778883080318 chrX 155270560 4447975 0.028646608861332117 0.2063248605824401 chrY 59373566 226763 0.0038192585569140312 0.10441752118299612