BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716710.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 = 8,745,169 number of mapped reads = 8,178,770 (93.52%) number of supplementary alignments = 164,441 (1.88%) number of secondary alignments = 0 number of mapped bases = 629,637,730 bp number of sequenced bases = 629,402,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,165,118 duplication rate = 10.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4433 >>>>>>> ACTG content number of A's = 155,206,704 bp (24.66%) number of C's = 134,538,946 bp (21.38%) number of T's = 189,129,746 bp (30.05%) number of G's = 150,502,955 bp (23.91%) number of N's = 24,147 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 4,128,277 number of insertions = 56,659 mapped reads with insertion percentage = 0.68% number of deletions = 115,808 mapped reads with deletion percentage = 1.39% homopolymer indels = 38% >>>>>>> Coverage mean coverageData = 0.2034X std coverageData = 1.4004X There is a 11.22% of reference with a coverageData >= 1X There is a 4.25% of reference with a coverageData >= 2X There is a 1.96% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 70415877 0.28251033725609054 2.894094822400283 chr2 243199373 52969579 0.21780310675389775 1.5092826716300372 chr3 198022430 41336362 0.20874585772934914 0.7810102751339149 chr4 191154276 29909695 0.15646887752592048 1.154866650306981 chr5 180915260 37648685 0.20810121268929996 0.812437733950356 chr6 171115067 38134684 0.22285988410360147 0.9086229602234348 chr7 159138663 39438034 0.24782182567412922 2.002002593120861 chr8 146364022 36324852 0.24818156472906983 1.324741830376275 chr9 141213431 18659841 0.1321392793012727 0.942546293581282 chr10 135534747 33203724 0.24498311123124758 1.8640072511131436 chr11 135006516 27321706 0.20237323952571296 1.1779289841101621 chr12 133851895 21975732 0.16417946118730706 0.6773116238778637 chr13 115169878 11864895 0.10302081764817013 0.5156204313704464 chr14 107349540 12070845 0.1124443104274131 0.6537511412155733 chr15 102531392 13117453 0.1279359691127572 0.5965996141299672 chr16 90354753 18785780 0.20791136466279753 0.8697724866576952 chr17 81195210 11436854 0.1408562647969012 0.7857438807514897 chr18 78077248 18504926 0.23700791810694968 1.5640716009761095 chr19 59128983 15646590 0.26461794548368944 2.093084105269715 chr20 63025520 16766343 0.26602466746803516 0.9729811749060293 chr21 48129895 10884639 0.22615131406374353 1.0895313119943826 chr22 51304566 9743488 0.18991463644775788 0.7683859888120381 chrMT 16571 25273 1.5251342707138977 2.0523360594845093 chrX 155270560 41446066 0.2669280383866716 0.978023969084329 chrY 59373566 2005807 0.0337828285402295 1.0548535102380687