BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524916.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 = 2,031,746 number of mapped reads = 1,881,541 (92.61%) number of supplementary alignments = 8,200 (0.4%) number of secondary alignments = 0 number of mapped bases = 110,402,185 bp number of sequenced bases = 110,367,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,451 duplication rate = 5.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1203 >>>>>>> ACTG content number of A's = 28,224,521 bp (25.57%) number of C's = 22,739,655 bp (20.6%) number of T's = 33,395,315 bp (30.26%) number of G's = 26,006,740 bp (23.56%) number of N's = 838 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 560,935 number of insertions = 8,247 mapped reads with insertion percentage = 0.44% number of deletions = 20,826 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3239X There is a 2.95% of reference with a coverageData >= 1X There is a 0.44% 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 11460012 0.04597786739315687 0.5831251394327115 chr2 243199373 9830994 0.040423599282881376 0.39673914804465404 chr3 198022430 7876100 0.039773777142316655 0.232672676457552 chr4 191154276 4854411 0.02539525194822218 0.24798101356441876 chr5 180915260 6674917 0.03689526798347469 0.2248357459408469 chr6 171115067 7060727 0.0412630350078991 0.24951623636034073 chr7 159138663 6638690 0.04171638667091227 0.38834056665284633 chr8 146364022 8870637 0.06060667696054431 0.44943553949977877 chr9 141213431 4005974 0.02836822228333224 0.24925593658852796 chr10 135534747 4772041 0.035208985928899844 0.37105087337310577 chr11 135006516 5520804 0.0408928706818862 0.2798078253418591 chr12 133851895 3695577 0.02760944848782305 0.20047380783931185 chr13 115169878 2650761 0.023016096274756842 0.17858302822069963 chr14 107349540 2009728 0.018721347105912143 0.16762382295225806 chr15 102531392 2818080 0.02748504575067117 0.19577239279324296 chr16 90354753 3405432 0.03768957234601704 0.24247722204579406 chr17 81195210 2591195 0.031913151034402155 0.22140322132178294 chr18 78077248 2854279 0.03655711584506667 0.410911699040304 chr19 59128983 2312092 0.039102515935374706 0.4061561880007656 chr20 63025520 2188423 0.03472280752304781 0.22768064965665005 chr21 48129895 968433 0.020121236499684864 0.21348679724690425 chr22 51304566 1937535 0.03776535211310432 0.23113307611683986 chrMT 16571 22306 1.3460865367207773 1.5308838781476681 chrX 155270560 5027759 0.03238063287721768 0.22889952379923606 chrY 59373566 355278 0.005983773991274164 0.22467150217967655