BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524918.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 = 873,507 number of mapped reads = 807,788 (92.48%) number of supplementary alignments = 3,020 (0.35%) number of secondary alignments = 0 number of mapped bases = 47,442,587 bp number of sequenced bases = 47,426,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,156 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1441 >>>>>>> ACTG content number of A's = 12,172,767 bp (25.67%) number of C's = 9,383,108 bp (19.78%) number of T's = 14,781,849 bp (31.17%) number of G's = 11,088,719 bp (23.38%) number of N's = 342 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 240,246 number of insertions = 3,461 mapped reads with insertion percentage = 0.43% number of deletions = 9,372 mapped reads with deletion percentage = 1.15% homopolymer indels = 40.96% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1701X There is a 1.4% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4908720 0.019693912818776887 0.28471381603567797 chr2 243199373 4134383 0.01699997392674199 0.20276153903272934 chr3 198022430 3378595 0.01706167831593623 0.13949266254219078 chr4 191154276 2156820 0.011283137605564209 0.136376290315708 chr5 180915260 2985997 0.016504948228247853 0.13737972137304627 chr6 171115067 2992490 0.017488173615944645 0.14679292394488794 chr7 159138663 2903301 0.018243844363578697 0.2015464286004374 chr8 146364022 4126319 0.028192167334674636 0.22093430784557475 chr9 141213431 1706253 0.012082795438912606 0.14044144035540007 chr10 135534747 2027902 0.014962229574973862 0.1850275384331003 chr11 135006516 2407804 0.01783472436248929 0.158437186237974 chr12 133851895 1577445 0.011785003118558762 0.11764691454095401 chr13 115169878 1119168 0.009717540900755318 0.10507122866617535 chr14 107349540 853018 0.007946172848062507 0.09821424401348781 chr15 102531392 1030390 0.010049507569350078 0.10782928781862416 chr16 90354753 1451039 0.016059354398323684 0.14033161065368713 chr17 81195210 1093000 0.013461385222108546 0.12761385654375862 chr18 78077248 1215361 0.015566135220339733 0.20689381069308 chr19 59128983 994199 0.01681407238139036 0.2050679322539584 chr20 63025520 786499 0.012479056102988124 0.12301523405151854 chr21 48129895 429664 0.008927175095644817 0.11791802918245226 chr22 51304566 849055 0.016549306742015907 0.13838374240977216 chrMT 16571 17272 1.042302818176332 1.221297557474655 chrX 155270560 2147207 0.0138288095309246 0.13186354599809458 chrY 59373566 150686 0.002537930768719534 0.11032151895238886