BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524317.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 = 2,997,777 number of mapped reads = 2,757,007 (91.97%) number of supplementary alignments = 10,776 (0.36%) number of secondary alignments = 0 number of mapped bases = 161,049,119 bp number of sequenced bases = 161,004,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,597 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1693 >>>>>>> ACTG content number of A's = 40,514,511 bp (25.16%) number of C's = 31,959,389 bp (19.85%) number of T's = 49,988,308 bp (31.05%) number of G's = 38,518,787 bp (23.92%) number of N's = 23,261 bp (0.01%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 818,883 number of insertions = 12,930 mapped reads with insertion percentage = 0.47% number of deletions = 28,538 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.4374X There is a 4.45% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13595302 0.05454470663084125 0.8250692120159653 chr2 243199373 10339754 0.04251554546565381 0.644486040114892 chr3 198022430 11142507 0.05626891357711346 0.26962941945528623 chr4 191154276 8267308 0.04324940133695989 0.2745004229605292 chr5 180915260 9351732 0.051691228257914786 0.26015869893041593 chr6 171115067 10180721 0.059496344643923144 0.3090744226316791 chr7 159138663 7315395 0.04596868455530508 0.5437645285352447 chr8 146364022 16886519 0.11537342831423422 0.5407038804662238 chr9 141213431 6708870 0.04750872457733854 0.331161937969366 chr10 135534747 8168103 0.060265748679192946 0.41097900273842325 chr11 135006516 7815206 0.05788762077231887 0.37141330656351135 chr12 133851895 6381257 0.04767401313220108 0.25604854456961146 chr13 115169878 4064733 0.03529336898316416 0.21450853521066954 chr14 107349540 3359635 0.03129622166988326 0.21529867809459416 chr15 102531392 4989896 0.04866700727129502 0.25759398379412674 chr16 90354753 5103813 0.0564863809654817 0.2915333170544677 chr17 81195210 5100158 0.06281353296579933 0.3257011518287871 chr18 78077248 3781961 0.04843870777822497 0.6219697597134968 chr19 59128983 2956601 0.050002568114523464 0.5431582094449878 chr20 63025520 3769456 0.05980840776878953 0.28688189300544414 chr21 48129895 2330606 0.048423251286960005 0.2777860005132033 chr22 51304566 1199537 0.02338070650475827 0.1745407370431297 chrMT 16571 2663 0.16070243195944722 0.4194194849365689 chrX 155270560 7788195 0.05015886462958593 0.2968110825544447 chrY 59373566 449191 0.007565504824150195 0.19859953444461415