BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716108.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 = 717,840 number of mapped reads = 626,495 (87.28%) number of supplementary alignments = 2,272 (0.32%) number of secondary alignments = 0 number of mapped bases = 35,607,184 bp number of sequenced bases = 35,596,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,613 duplication rate = 1.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0765 >>>>>>> ACTG content number of A's = 8,917,179 bp (25.05%) number of C's = 6,898,211 bp (19.38%) number of T's = 11,241,995 bp (31.58%) number of G's = 8,538,462 bp (23.99%) number of N's = 266 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 187,287 number of insertions = 2,763 mapped reads with insertion percentage = 0.44% number of deletions = 6,930 mapped reads with deletion percentage = 1.1% homopolymer indels = 38.35% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 0.1291X There is a 1.09% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3012005 0.012084242710873728 0.15205569294702204 chr2 243199373 2793751 0.011487492609612937 0.16987115989259954 chr3 198022430 2045410 0.010329183416242291 0.10626365654542286 chr4 191154276 2179794 0.011403323250796649 0.11619879834841844 chr5 180915260 2007605 0.011096935659269428 0.10885650920256017 chr6 171115067 1880905 0.010992047824754088 0.11682941947093631 chr7 159138663 2016019 0.012668316812489495 0.16515079724113108 chr8 146364022 1838926 0.012564057579669408 0.12758340850321775 chr9 141213431 1186125 0.008399519731235764 0.10055630865259693 chr10 135534747 1592937 0.011752978739835622 0.15093095223419437 chr11 135006516 1262674 0.00935268931760301 0.1089935290258414 chr12 133851895 1754018 0.013104170097853302 0.11901114232757101 chr13 115169878 1076871 0.009350283413515468 0.10050980999928973 chr14 107349540 1201469 0.011192120618309124 0.11105513391947906 chr15 102531392 1299593 0.012675074186060013 0.11873414430849644 chr16 90354753 1256493 0.013906219189155439 0.12590717310839675 chr17 81195210 1595575 0.01965109764479949 0.14923110236125212 chr18 78077248 660162 0.008455241660156874 0.1383220725409963 chr19 59128983 975550 0.0164986771377414 0.1590682398009561 chr20 63025520 1156766 0.018353930280940164 0.14310384677033372 chr21 48129895 451679 0.009384583116169274 0.10369304058378252 chr22 51304566 342464 0.006675117376492377 0.08454807601381886 chrMT 16571 1258 0.07591575644197694 0.3061979011395966 chrX 155270560 1905448 0.012271791896673781 0.11810806505141656 chrY 59373566 113687 0.0019147746658841412 0.06702231015299798