BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716749.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 = 619,390 number of mapped reads = 456,039 (73.63%) number of supplementary alignments = 399 (0.06%) number of secondary alignments = 0 number of mapped bases = 23,783,340 bp number of sequenced bases = 23,777,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,846 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1888 >>>>>>> ACTG content number of A's = 5,091,047 bp (21.41%) number of C's = 4,111,379 bp (17.29%) number of T's = 8,010,178 bp (33.69%) number of G's = 6,564,124 bp (27.61%) number of N's = 453 bp (0%) GC percentage = 44.9% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 162,059 number of insertions = 1,513 mapped reads with insertion percentage = 0.33% number of deletions = 3,704 mapped reads with deletion percentage = 0.81% homopolymer indels = 39.2% >>>>>>> Coverage mean coverageData = 0.0077X std coverageData = 0.101X There is a 0.71% of reference with a coverageData >= 1X There is a 0.05% 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 1921095 0.007707483304525047 0.10081048035363317 chr2 243199373 1999512 0.008221698828146239 0.13753672898439737 chr3 198022430 1536695 0.007760206760415979 0.09468705297026442 chr4 191154276 1479345 0.007739010766361303 0.09745529358064764 chr5 180915260 1396694 0.0077201558342839625 0.09426470321231316 chr6 171115067 1346609 0.00786961092093661 0.10297460663815584 chr7 159138663 1286189 0.00808219056107063 0.10286503263834221 chr8 146364022 1179747 0.008060361992512068 0.09805129504661261 chr9 141213431 1003328 0.007105046544758196 0.09425159273571415 chr10 135534747 1161519 0.008569898315448216 0.10775643347209245 chr11 135006516 1078584 0.007989125502653516 0.09928009674840563 chr12 133851895 1085615 0.00811056877453995 0.09691235359275682 chr13 115169878 713554 0.006195665154737769 0.08466073847612084 chr14 107349540 729519 0.00679573475582662 0.08923779053867781 chr15 102531392 697330 0.006801136572884917 0.08919050041104093 chr16 90354753 747769 0.008275923237817938 0.10086373826669116 chr17 81195210 714635 0.008801442843734254 0.10236118995197138 chr18 78077248 594164 0.007609950596619389 0.10234062470781606 chr19 59128983 581588 0.009835920905319815 0.11454881931084009 chr20 63025520 547232 0.008682705037578429 0.10182188617221047 chr21 48129895 307964 0.006398601118909567 0.0884616443816101 chr22 51304566 336800 0.006564717845971058 0.08846542940534322 chrMT 16571 3246 0.19588437632007724 0.4637320748913805 chrX 155270560 1250086 0.008051017527083048 0.09730515084959415 chrY 59373566 84521 0.0014235459598300024 0.04823104770968952