BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716570.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 = 2,878,491 number of mapped reads = 2,720,593 (94.51%) number of supplementary alignments = 66,437 (2.31%) number of secondary alignments = 0 number of mapped bases = 210,512,448 bp number of sequenced bases = 210,429,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,833 duplication rate = 5.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4863 >>>>>>> ACTG content number of A's = 50,749,160 bp (24.12%) number of C's = 44,012,070 bp (20.92%) number of T's = 61,790,739 bp (29.36%) number of G's = 53,869,029 bp (25.6%) number of N's = 8,441 bp (0%) GC percentage = 46.51% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,374,424 number of insertions = 17,787 mapped reads with insertion percentage = 0.64% number of deletions = 38,782 mapped reads with deletion percentage = 1.4% homopolymer indels = 38.94% >>>>>>> Coverage mean coverageData = 0.068X std coverageData = 0.5166X There is a 5.24% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 17215585 0.06906937656135267 0.7532664176243872 chr2 243199373 17659385 0.07261279000090186 0.6075523168557821 chr3 198022430 13595262 0.06865516194301827 0.32669974275165886 chr4 191154276 13359912 0.06989073056362077 0.5897811389952724 chr5 180915260 12162765 0.06722907177647701 0.32532459884608417 chr6 171115067 11790226 0.06890232524059381 0.3513667084087169 chr7 159138663 11422947 0.0717798351743096 0.6396562933828757 chr8 146364022 10507401 0.07178950712354706 0.509478822861863 chr9 141213431 8744109 0.06192122759201283 0.4625186559984138 chr10 135534747 10423609 0.07690728193855706 0.8166721863610898 chr11 135006516 9538293 0.07065061215267565 0.5060230580790431 chr12 133851895 9472361 0.07076747774097632 0.34024141686719755 chr13 115169878 6218611 0.053995116674517965 0.288563953869455 chr14 107349540 6315898 0.05883488648391041 0.34776757107015266 chr15 102531392 6045529 0.05896271261000728 0.30270171970450105 chr16 90354753 6628739 0.07336347873143984 0.39215274652881404 chr17 81195210 6094840 0.07506403394978596 0.4185977267068603 chr18 78077248 5599669 0.07171960005557573 0.7545247504593013 chr19 59128983 4748114 0.08030095833036736 0.5713457275267699 chr20 63025520 4863234 0.07716293336413567 0.3961424906627356 chr21 48129895 2894986 0.060149435189916785 0.501636804941963 chr22 51304566 2984315 0.05816860433046057 0.3248767533431648 chrMT 16571 15742 0.949972844125279 1.275004627931697 chrX 155270560 11371435 0.07323625933982592 0.3810308181497749 chrY 59373566 839481 0.014138968846843392 0.5702327693559953