BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524829.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 = 983,937 number of mapped reads = 886,353 (90.08%) number of supplementary alignments = 4,939 (0.5%) number of secondary alignments = 0 number of mapped bases = 50,546,439 bp number of sequenced bases = 50,531,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,076 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8091 >>>>>>> ACTG content number of A's = 12,717,453 bp (25.17%) number of C's = 9,347,517 bp (18.5%) number of T's = 16,200,783 bp (32.06%) number of G's = 12,259,942 bp (24.26%) number of N's = 6,084 bp (0.01%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 256,710 number of insertions = 4,063 mapped reads with insertion percentage = 0.46% number of deletions = 9,375 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.37% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1656X There is a 1.53% of reference with a coverageData >= 1X There is a 0.07% 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 4088467 0.01640303636394952 0.21036554873666408 chr2 243199373 4245417 0.01745652938011481 0.2224177478003211 chr3 198022430 3321515 0.016773428141448422 0.13678320786986534 chr4 191154276 3266327 0.017087386525426195 0.14708339938281406 chr5 180915260 3045745 0.016835202293051455 0.13689481257885167 chr6 171115067 2889946 0.01688890435346643 0.14061633020568529 chr7 159138663 2798668 0.017586348579540348 0.21128286154051712 chr8 146364022 2541660 0.017365333128109856 0.15764100787486215 chr9 141213431 2174173 0.01539636127104652 0.15861331897358363 chr10 135534747 2413251 0.017805404543234954 0.18897867529636603 chr11 135006516 2284552 0.016921790648978752 0.1622086597039012 chr12 133851895 2305608 0.017225068050026486 0.1389968998472331 chr13 115169878 1573190 0.013659734883108933 0.12211801244804536 chr14 107349540 1518554 0.014145882693116337 0.13009705859113463 chr15 102531392 1458572 0.014225613946604763 0.12795621765741577 chr16 90354753 1541377 0.017059168984724024 0.1482658031401735 chr17 81195210 1382020 0.017020954807555767 0.1430354999436008 chr18 78077248 1351356 0.017307935853476803 0.23970786810770287 chr19 59128983 1040185 0.01759179588798272 0.17438856118398896 chr20 63025520 1058660 0.016797322735298336 0.13949312523673607 chr21 48129895 665581 0.013828847954062647 0.1300933393827667 chr22 51304566 592169 0.011542228034830272 0.11235614047467647 chrMT 16571 7946 0.4795124011827892 0.804299947749837 chrX 155270560 2826306 0.018202458985141806 0.1538948271854983 chrY 59373566 155194 0.002613856812979702 0.07785411426057533