BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716102.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 = 1,672,820 number of mapped reads = 1,518,901 (90.8%) number of supplementary alignments = 7,325 (0.44%) number of secondary alignments = 0 number of mapped bases = 87,371,249 bp number of sequenced bases = 87,348,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,743 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4129 >>>>>>> ACTG content number of A's = 21,437,000 bp (24.54%) number of C's = 17,640,125 bp (20.2%) number of T's = 28,214,602 bp (32.3%) number of G's = 20,054,682 bp (22.96%) number of N's = 2,343 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 430,363 number of insertions = 5,639 mapped reads with insertion percentage = 0.37% number of deletions = 14,668 mapped reads with deletion percentage = 0.96% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2596X There is a 2.5% of reference with a coverageData >= 1X There is a 0.23% 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 10246218 0.04110809417000409 0.39476287269209237 chr2 243199373 7792825 0.032042948564674135 0.36583829245779914 chr3 198022430 6312697 0.03187869677187579 0.20087227285489614 chr4 191154276 4202385 0.021984258411253118 0.17161938344858635 chr5 180915260 4012088 0.022176614620568767 0.1661579886250626 chr6 171115067 6891180 0.04027219882396446 0.26642208094130115 chr7 159138663 5252038 0.03300290388891856 0.36069828409643845 chr8 146364022 6504662 0.044441672967964765 0.259338381493522 chr9 141213431 2621553 0.01856447351668695 0.20513139947878056 chr10 135534747 4588732 0.03385649880616961 0.3217997733375046 chr11 135006516 3017843 0.02235331367265266 0.2083370083412441 chr12 133851895 4016789 0.03000920532354062 0.19575178336869084 chr13 115169878 2071100 0.017983000728714848 0.14897882974468094 chr14 107349540 2024189 0.01885605657928297 0.16663892085563753 chr15 102531392 2740509 0.02672848721296986 0.18351257847090466 chr16 90354753 1954182 0.02162788270806296 0.18515550853501733 chr17 81195210 2130268 0.0262363752738616 0.18607566166813064 chr18 78077248 1764197 0.022595532567951167 0.36741169301235765 chr19 59128983 1435968 0.024285349200069955 0.30764642020320654 chr20 63025520 1565410 0.024837716531335242 0.17455374790957925 chr21 48129895 839726 0.01744707733104342 0.15961742022721448 chr22 51304566 1136388 0.022149841400081232 0.16438298077778116 chrMT 16571 179774 10.848711604610465 5.977717196480147 chrX 155270560 3867366 0.024907271539434134 0.19983487242498307 chrY 59373566 203162 0.0034217584303425533 0.08456093135584898