BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716184.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 = 2,621,360 number of mapped reads = 2,316,242 (88.36%) number of supplementary alignments = 8,443 (0.32%) number of secondary alignments = 0 number of mapped bases = 131,367,640 bp number of sequenced bases = 131,328,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,077 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8435 >>>>>>> ACTG content number of A's = 33,134,835 bp (25.23%) number of C's = 27,026,636 bp (20.58%) number of T's = 39,795,173 bp (30.3%) number of G's = 31,371,283 bp (23.89%) number of N's = 1,007 bp (0%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 686,405 number of insertions = 10,908 mapped reads with insertion percentage = 0.47% number of deletions = 24,346 mapped reads with deletion percentage = 1.04% homopolymer indels = 39.2% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.3313X There is a 3.7% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 11049328 0.04433019246118548 0.39883553709648806 chr2 243199373 10202552 0.04195139105066689 0.4911322839893763 chr3 198022430 7519812 0.037974546620804524 0.22285434541003765 chr4 191154276 7982495 0.04175943728300381 0.262536083827168 chr5 180915260 7427746 0.041056492415288796 0.2260621174374332 chr6 171115067 6901951 0.04033514477132513 0.27168902556312885 chr7 159138663 7479343 0.04699890560221685 0.4765833727587868 chr8 146364022 6794496 0.04642190004863354 0.3033512137894561 chr9 141213431 4348145 0.03079129916473738 0.23989580858835263 chr10 135534747 5788327 0.04270732877082804 0.423294214465054 chr11 135006516 4613945 0.03417572082224535 0.2702156183081705 chr12 133851895 6592366 0.049251196630424994 0.24917736188905093 chr13 115169878 3881390 0.03370143363354088 0.20664391923926434 chr14 107349540 4373824 0.040743760988635816 0.2402687884345862 chr15 102531392 4848975 0.04729258918088228 0.2510663283204543 chr16 90354753 4662808 0.05160556412566365 0.27831451234306975 chr17 81195210 5881358 0.0724347901803567 0.32569527605865917 chr18 78077248 2419391 0.03098714493625595 0.3979994812356169 chr19 59128983 3607196 0.06100554782077006 0.40538000309244104 chr20 63025520 4279750 0.0679050327549856 0.3116756177217747 chr21 48129895 1625777 0.033778943419677104 0.23155376208174827 chr22 51304566 1253855 0.024439442680403923 0.17589105180888945 chrMT 16571 451476 27.2449459899825 18.33704556716677 chrX 155270560 6976156 0.04492903226471264 0.25977069372300543 chrY 59373566 405178 0.006824215341891373 0.1885324509893164