BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716812.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 = 1,654,233 number of mapped reads = 1,527,205 (92.32%) number of supplementary alignments = 7,555 (0.46%) number of secondary alignments = 0 number of mapped bases = 88,965,946 bp number of sequenced bases = 88,939,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,637 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.863 >>>>>>> ACTG content number of A's = 21,517,093 bp (24.19%) number of C's = 18,059,238 bp (20.3%) number of T's = 28,618,945 bp (32.18%) number of G's = 20,742,221 bp (23.32%) number of N's = 2,440 bp (0%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 439,717 number of insertions = 5,170 mapped reads with insertion percentage = 0.34% number of deletions = 16,471 mapped reads with deletion percentage = 1.07% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2624X There is a 2.59% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 9168677 0.03678497154075295 0.4673097000509452 chr2 243199373 7831910 0.03220366032769336 0.34171433566760484 chr3 198022430 8742098 0.044147009002970014 0.23052026339067563 chr4 191154276 4034693 0.021106998412109806 0.16736812178942068 chr5 180915260 4058912 0.02243543192542188 0.16433312926822644 chr6 171115067 6552968 0.03829568088238542 0.299852033801575 chr7 159138663 4886165 0.030703820855903508 0.24638083017769302 chr8 146364022 6101800 0.04168920692818895 0.25171325413639106 chr9 141213431 3384163 0.023964880507718844 0.22742197046059934 chr10 135534747 4744281 0.035004167602865705 0.2942393695225089 chr11 135006516 3048436 0.022579917550053657 0.22006979468010499 chr12 133851895 3740546 0.02794540936458165 0.18688144116268962 chr13 115169878 2072363 0.01799396713783095 0.14634484956140364 chr14 107349540 1994676 0.018581132252639368 0.16367946454923737 chr15 102531392 2651076 0.02585623727804261 0.1773399410018257 chr16 90354753 1900455 0.02103325986625186 0.17759404938062695 chr17 81195210 2003808 0.024678894235263385 0.17698607415361053 chr18 78077248 1874897 0.024013359179872733 0.39860589512613703 chr19 59128983 1560426 0.02639020529069475 0.31774742361197633 chr20 63025520 1301626 0.02065236431210722 0.15870920710368944 chr21 48129895 818502 0.017006104002512366 0.1574434680685555 chr22 51304566 1393950 0.027170096322420893 0.17964444191047105 chrMT 16571 28432 1.7157685112546015 1.5720193048158182 chrX 155270560 4852217 0.03125007728445109 0.22017667226929288 chrY 59373566 218869 0.0036863037668985557 0.08695105029362983