BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717042.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 = 8,384,847 number of mapped reads = 7,833,136 (93.42%) number of supplementary alignments = 172,103 (2.05%) number of secondary alignments = 0 number of mapped bases = 586,544,130 bp number of sequenced bases = 586,339,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 692,758 duplication rate = 6.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9623 >>>>>>> ACTG content number of A's = 153,523,345 bp (26.18%) number of C's = 122,524,327 bp (20.9%) number of T's = 173,280,369 bp (29.55%) number of G's = 136,941,090 bp (23.36%) number of N's = 70,506 bp (0.01%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 4,309,593 number of insertions = 44,995 mapped reads with insertion percentage = 0.57% number of deletions = 121,094 mapped reads with deletion percentage = 1.53% homopolymer indels = 40.7% >>>>>>> Coverage mean coverageData = 0.1895X std coverageData = 1.3524X There is a 12.24% of reference with a coverageData >= 1X There is a 3.77% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 59129621 0.23722958347213105 2.4065585909854206 chr2 243199373 45624431 0.18760094007314732 2.1759955358492697 chr3 198022430 46868885 0.23668472808863117 0.7215253377514671 chr4 191154276 23539398 0.12314345508023058 0.5998878657709593 chr5 180915260 36707364 0.20289810820822965 0.6571063248884219 chr6 171115067 36705153 0.2145056752950925 0.9550189673332534 chr7 159138663 31740262 0.19945034978709103 2.1828089064682783 chr8 146364022 38515517 0.2631488016911697 1.6597761768925732 chr9 141213431 27269101 0.19310557648018623 1.1949305333038305 chr10 135534747 31804481 0.23465924203186064 1.3183628594882937 chr11 135006516 24093684 0.1784631195134315 1.0678462908889368 chr12 133851895 24912274 0.18611820176322494 0.6444152354124721 chr13 115169878 21747448 0.1888293048291672 0.634389103993845 chr14 107349540 14561910 0.13564948671414895 0.6196643215907698 chr15 102531392 10527155 0.10267250638711703 0.46743954876301236 chr16 90354753 15814467 0.17502639844524837 0.6778536925268305 chr17 81195210 18924695 0.2330764955223344 0.880352114839486 chr18 78077248 15713253 0.20125264917124128 1.62315021894183 chr19 59128983 11289195 0.1909248971862073 2.06328188562786 chr20 63025520 10400649 0.16502281932778975 0.6161191812598711 chr21 48129895 6184302 0.1284919071608197 0.5725446427337401 chr22 51304566 8005862 0.15604579912049155 0.6002719152803718 chrMT 16571 35283 2.1292016172832056 4.354490360438697 chrX 155270560 25223519 0.1624488183722658 0.7870390503235873 chrY 59373566 1206221 0.020315791711078966 0.5750680901309845