BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525108.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 = 781,491 number of mapped reads = 689,760 (88.26%) number of supplementary alignments = 19,369 (2.48%) number of secondary alignments = 0 number of mapped bases = 53,022,977 bp number of sequenced bases = 53,002,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,814 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.242 >>>>>>> ACTG content number of A's = 13,655,341 bp (25.76%) number of C's = 10,251,326 bp (19.34%) number of T's = 16,452,787 bp (31.04%) number of G's = 12,640,987 bp (23.85%) number of N's = 1,951 bp (0%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 396,860 number of insertions = 4,506 mapped reads with insertion percentage = 0.64% number of deletions = 12,086 mapped reads with deletion percentage = 1.73% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.2013X There is a 1.6% 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 4193299 0.016823625085371403 0.3005488511944013 chr2 243199373 4608755 0.01895052171865591 0.26936975759213805 chr3 198022430 3529167 0.017822056824572854 0.13920124430779865 chr4 191154276 3447492 0.018035128861046246 0.14336958981386683 chr5 180915260 3262237 0.01803185093396765 0.1422250630397449 chr6 171115067 3098072 0.01810519701342255 0.1523990833345753 chr7 159138663 2963454 0.018621835474387515 0.2868408758891671 chr8 146364022 2753101 0.018809957272149846 0.2544125171328385 chr9 141213431 2218695 0.015711642896064186 0.19612846854707572 chr10 135534747 2503369 0.01847031152830499 0.19953904387690086 chr11 135006516 2389200 0.01769692360626505 0.20726075766614024 chr12 133851895 2386460 0.017829108807163322 0.13982406196408237 chr13 115169878 1700909 0.014768696724676568 0.12619676882775824 chr14 107349540 1657109 0.015436572900079498 0.14130944690406216 chr15 102531392 1513759 0.014763858857977857 0.12755509433101087 chr16 90354753 1472926 0.01630158847315979 0.14010980215699523 chr17 81195210 1352676 0.0166595541781344 0.1500851432323787 chr18 78077248 1495354 0.019152237537880434 0.3176453279941104 chr19 59128983 1009877 0.017079221538445877 0.22658139168949834 chr20 63025520 1030908 0.016356993167212265 0.13559821872741767 chr21 48129895 728256 0.015131053163527575 0.1332615154459105 chr22 51304566 565287 0.01101825907658979 0.10982167834872687 chrMT 16571 6446 0.388992818779796 0.7414775288861188 chrX 155270560 2984918 0.019223979098162588 0.17947481137129914 chrY 59373566 151251 0.0025474467880201098 0.06183314917548467