BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237813.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 = 1,519,138 number of mapped reads = 1,416,926 (93.27%) number of supplementary alignments = 7,519 (0.49%) number of secondary alignments = 0 number of mapped bases = 103,023,158 bp number of sequenced bases = 102,976,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,059 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8334 >>>>>>> ACTG content number of A's = 31,176,388 bp (30.28%) number of C's = 20,656,843 bp (20.06%) number of T's = 30,022,427 bp (29.15%) number of G's = 20,949,174 bp (20.34%) number of N's = 171,951 bp (0.17%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 923,818 number of insertions = 8,217 mapped reads with insertion percentage = 0.58% number of deletions = 25,609 mapped reads with deletion percentage = 1.79% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.4092X There is a 2.86% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9003842 0.03612364921650486 0.9482962556574148 chr2 243199373 7893002 0.03245486163321647 0.35656344125013334 chr3 198022430 6765819 0.03416693250355528 0.20954654535335293 chr4 191154276 7265793 0.03801009923523761 0.23412563537678835 chr5 180915260 5982472 0.033067813074474754 0.20715890764200207 chr6 171115067 6379575 0.03728236859469541 0.2620828326076263 chr7 159138663 5660057 0.035566825140412296 0.5282739480077615 chr8 146364022 5409244 0.036957470326963275 0.3421300426535621 chr9 141213431 4168971 0.029522482178058546 0.36666211436327223 chr10 135534747 4711612 0.03476312978250515 0.36195269133506996 chr11 135006516 4550715 0.033707373057460424 0.330513106165036 chr12 133851895 4866944 0.036360665644666446 0.22052730449722519 chr13 115169878 3490730 0.0303094008660841 0.19350631449882189 chr14 107349540 3381737 0.031502109836707266 0.2149079718611693 chr15 102531392 2589680 0.025257435303326418 0.17652087422185392 chr16 90354753 2551673 0.028240606224666454 0.24368529718385798 chr17 81195210 2292749 0.028237490856911386 0.22885582412003808 chr18 78077248 3087845 0.03954858911010798 0.7875753067632819 chr19 59128983 1790273 0.03027741911272176 0.5137716708505452 chr20 63025520 2580440 0.04094278000403646 0.23972501624970555 chr21 48129895 1520274 0.031586896252318857 0.22289454097301184 chr22 51304566 1210720 0.023598679306633254 0.17077181506338013 chrMT 16571 133253 8.041337275964034 5.030934955399143 chrX 155270560 5249489 0.03380865632222876 0.2307154752884062 chrY 59373566 486249 0.008189654635195737 0.16748400101399566