BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231793.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,823,431 number of mapped reads = 2,485,114 (88.02%) number of supplementary alignments = 18,073 (0.64%) number of secondary alignments = 0 number of mapped bases = 156,940,391 bp number of sequenced bases = 156,882,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,992 duplication rate = 12.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.689 >>>>>>> ACTG content number of A's = 40,438,413 bp (25.78%) number of C's = 27,237,018 bp (17.36%) number of T's = 52,719,317 bp (33.6%) number of G's = 36,428,879 bp (23.22%) number of N's = 58,456 bp (0.04%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 996,737 number of insertions = 10,381 mapped reads with insertion percentage = 0.41% number of deletions = 35,748 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.6098X There is a 3.39% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 10562876 0.04237853433472489 0.7153856841338451 chr2 243199373 9940188 0.040872588927274904 1.1396602454654332 chr3 198022430 53657221 0.27096536993309295 0.7413064686773485 chr4 191154276 1886799 0.009870556073775719 0.16165196823708453 chr5 180915260 13704151 0.07574900536306335 0.3809700879897848 chr6 171115067 5960900 0.03483562321253686 0.505726077202777 chr7 159138663 7183104 0.04513739065408637 0.38497424513825856 chr8 146364022 1142294 0.007804472604613174 0.39239784901600167 chr9 141213431 2875642 0.020363799531221645 0.21452348571671867 chr10 135534747 5290578 0.039034846171218364 0.6524129943579592 chr11 135006516 2925841 0.021671850268323346 0.2223938063178358 chr12 133851895 10664468 0.0796736422745453 0.40327823240130195 chr13 115169878 1047748 0.009097413474728176 0.32156140729606025 chr14 107349540 6125461 0.05706089658139196 0.3295893872802857 chr15 102531392 510268 0.00497670020904427 0.19200329224697202 chr16 90354753 608497 0.006734532271921545 0.16652430033368482 chr17 81195210 3000429 0.036953275938321976 0.26274632102387324 chr18 78077248 1209759 0.015494385765235989 1.8814936036617722 chr19 59128983 1458722 0.024670168942361143 0.539092326447907 chr20 63025520 465345 0.007383437693175717 0.1253125174039171 chr21 48129895 907308 0.01885123580676833 0.1935426810044016 chr22 51304566 236518 0.0046100770056216826 0.08233406860581334 chrMT 16571 171796 10.367268119003077 10.895233901615532 chrX 155270560 14958210 0.09633642076128275 0.47105611543677384 chrY 59373566 446268 0.007516274161467748 0.2004609370113478