BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013197.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 = 1,984,531 number of mapped reads = 1,582,963 (79.77%) number of supplementary alignments = 21,821 (1.1%) number of secondary alignments = 0 number of mapped bases = 100,079,023 bp number of sequenced bases = 100,026,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,242 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9932 >>>>>>> ACTG content number of A's = 29,783,300 bp (29.78%) number of C's = 18,171,597 bp (18.17%) number of T's = 29,896,045 bp (29.89%) number of G's = 22,174,941 bp (22.17%) number of N's = 772 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 866,704 number of insertions = 7,244 mapped reads with insertion percentage = 0.45% number of deletions = 30,901 mapped reads with deletion percentage = 1.93% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.5757X There is a 2.67% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 4973991 0.01995578177516356 0.37096794395883276 chr2 243199373 12207056 0.05019361624752215 0.34466943525094346 chr3 198022430 5414571 0.02734322066444695 0.19429089884024303 chr4 191154276 4111537 0.02150899831296476 0.1730831018900986 chr5 180915260 3084845 0.017051325576405218 0.15403937468818713 chr6 171115067 4648230 0.027164352511400997 0.2540858737250663 chr7 159138663 8126101 0.05106302168694229 0.5826839412224364 chr8 146364022 5180589 0.03539523531267814 2.2981862898547063 chr9 141213431 4269943 0.03023751331415494 0.26687358149089013 chr10 135534747 3748375 0.027656192105482737 0.26691989590664256 chr11 135006516 5483409 0.040615884051107574 0.33360164448897617 chr12 133851895 5081245 0.03796169639585603 0.23024145676843458 chr13 115169878 1283049 0.011140491092644901 0.12177903559227884 chr14 107349540 3710068 0.034560632490833215 0.22978612461050466 chr15 102531392 1677313 0.016359019099243283 0.15071045673098363 chr16 90354753 3839487 0.042493470155355303 0.2553180570144846 chr17 81195210 4527334 0.05575863403764828 0.35014247368138995 chr18 78077248 1366309 0.01749945131262823 0.34913068855357177 chr19 59128983 1880531 0.031803878649494105 0.3114775918856233 chr20 63025520 3848435 0.061061535073411534 0.2995986972480008 chr21 48129895 2538328 0.05273911360080881 0.28086005610451753 chr22 51304566 1001697 0.01952451951352634 0.1605624276766965 chrMT 16571 8101 0.4888660913644318 0.8017025585343011 chrX 155270560 7844873 0.050523891972824725 0.285822824810396 chrY 59373566 223606 0.003766086746415063 0.07484350046039812