BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525066.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 = 4,379,693 number of mapped reads = 4,097,047 (93.55%) number of supplementary alignments = 17,916 (0.41%) number of secondary alignments = 0 number of mapped bases = 247,478,123 bp number of sequenced bases = 247,392,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 280,317 duplication rate = 5.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4816 >>>>>>> ACTG content number of A's = 65,815,516 bp (26.6%) number of C's = 48,301,219 bp (19.52%) number of T's = 75,906,035 bp (30.68%) number of G's = 57,340,960 bp (23.18%) number of N's = 29,201 bp (0.01%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,177,501 number of insertions = 21,911 mapped reads with insertion percentage = 0.53% number of deletions = 52,390 mapped reads with deletion percentage = 1.27% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0799X std coverageData = 0.6599X There is a 6.3% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 20226434 0.0811489813700404 1.3566288621425338 chr2 243199373 22140095 0.09103680953980091 0.7978924738962165 chr3 198022430 17251877 0.08712082262600251 0.36128164462902196 chr4 191154276 16771748 0.08773932946182171 0.4722944583591472 chr5 180915260 15372196 0.08496904020147333 0.35749345017751105 chr6 171115067 14778899 0.08636819222938445 0.4165693246074277 chr7 159138663 13958265 0.08771133762761348 0.7557949258493092 chr8 146364022 12952018 0.08849181529050903 0.895712561653895 chr9 141213431 10744513 0.07608704727243686 0.5042944338952002 chr10 135534747 11948939 0.08816144394322734 0.7569610346871604 chr11 135006516 12429919 0.09206903020888266 0.47943919815085473 chr12 133851895 11093969 0.08288242015550097 0.3672999054970122 chr13 115169878 7893281 0.0685359847303129 0.3188380752052324 chr14 107349540 7592429 0.0707262369265858 0.3474192642272106 chr15 102531392 7205083 0.07027197094915087 0.32166839750546783 chr16 90354753 7271836 0.08048094603280029 0.41106876098827877 chr17 81195210 6488001 0.07990620382655578 0.39230326133655863 chr18 78077248 6692612 0.08571782652995147 0.9485670664861657 chr19 59128983 4891716 0.08272958119371003 0.9815439406291367 chr20 63025520 5059591 0.0802784491107729 0.36887084858031693 chr21 48129895 3389591 0.07042589642050955 0.42369545241333106 chr22 51304566 2892287 0.05637484585679957 0.2868489737855925 chrMT 16571 42906 2.589222135055217 2.1779163403226787 chrX 155270560 7638601 0.049195423781559104 0.3360669646713547 chrY 59373566 751317 0.012654065615664721 0.4554362335825982