BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013363.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 = 2,154,361 number of mapped reads = 1,863,578 (86.5%) number of supplementary alignments = 12,697 (0.59%) number of secondary alignments = 0 number of mapped bases = 124,349,394 bp number of sequenced bases = 124,298,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,147 duplication rate = 4.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3013 >>>>>>> ACTG content number of A's = 33,760,141 bp (27.16%) number of C's = 23,260,945 bp (18.71%) number of T's = 39,164,519 bp (31.51%) number of G's = 28,086,673 bp (22.6%) number of N's = 26,646 bp (0.02%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,022,792 number of insertions = 9,151 mapped reads with insertion percentage = 0.49% number of deletions = 29,291 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.4308X There is a 3.3% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 9993349 0.0400935771389713 0.8864498222240798 chr2 243199373 12077716 0.04966178921851085 0.5506899632838487 chr3 198022430 10869619 0.05489084746611785 0.2731247790242823 chr4 191154276 9225144 0.04826020214164605 0.28161611960572447 chr5 180915260 5526359 0.030546671408481517 0.20422005634278173 chr6 171115067 9772118 0.05710846023862995 0.3863099180754017 chr7 159138663 4079494 0.02563483897059007 0.44356716803747714 chr8 146364022 11013374 0.0752464564003304 0.4885960663641725 chr9 141213431 5785469 0.04096967943509566 0.4075530096499113 chr10 135534747 3024516 0.022315428825052514 0.3946276758301656 chr11 135006516 4394737 0.03255203622912541 0.3117330438098967 chr12 133851895 5200913 0.038855729311863686 0.2403147457084681 chr13 115169878 2191265 0.01902637250340753 0.16123984792627238 chr14 107349540 5752921 0.05359055101679989 0.29100749553599475 chr15 102531392 1190625 0.011612297236733116 0.1349444323228014 chr16 90354753 2641253 0.02923203165637562 0.22718115193394114 chr17 81195210 4864103 0.05990628018574002 0.3291991551769358 chr18 78077248 2746932 0.03518223388201387 0.7241164718469207 chr19 59128983 2321434 0.03926050952034808 0.5907333494064892 chr20 63025520 2079717 0.032998014137765146 0.22072545909541624 chr21 48129895 1799272 0.037383667676815 0.24478170125268803 chr22 51304566 1548804 0.03018842416481995 0.2001466844078636 chrMT 16571 36939 2.22913523625611 2.0637746953345832 chrX 155270560 5969054 0.038442921826262494 0.27121513329012137 chrY 59373566 244267 0.0041140698875994745 0.13204231508417452