BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,200,422 number of mapped reads = 3,526,410 (83.95%) number of supplementary alignments = 23,173 (0.55%) number of secondary alignments = 0 number of mapped bases = 238,382,572 bp number of sequenced bases = 238,296,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 256,266 duplication rate = 5.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.269 >>>>>>> ACTG content number of A's = 67,526,161 bp (28.34%) number of C's = 41,932,297 bp (17.6%) number of T's = 77,850,944 bp (32.67%) number of G's = 50,501,529 bp (21.19%) number of N's = 485,663 bp (0.2%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,339,558 number of insertions = 18,468 mapped reads with insertion percentage = 0.52% number of deletions = 48,760 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 0.077X std coverageData = 0.7175X There is a 5.44% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% 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% 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 20429434 0.0819634226708707 1.2342890435423874 chr2 243199373 16393613 0.06740812197735395 0.5909837391069894 chr3 198022430 21584746 0.10900152068631822 0.4412260322625959 chr4 191154276 15736189 0.0823219303762789 0.4108593609106395 chr5 180915260 14079843 0.0778256239965606 0.3774194557043204 chr6 171115067 21138009 0.1235309629396925 0.7547281687951202 chr7 159138663 12190928 0.07660569575100679 0.7288362289749795 chr8 146364022 19181894 0.1310560733292776 1.5561548005294867 chr9 141213431 12487208 0.0884279059829656 0.8389119882255941 chr10 135534747 6177515 0.045578828578917846 0.5008798542495282 chr11 135006516 10956161 0.08115283117149694 0.5006820519487388 chr12 133851895 9796461 0.07318881066271045 0.39959265138037114 chr13 115169878 6566484 0.05701563737004219 0.3122321609451542 chr14 107349540 6779347 0.06315208244022284 0.4163724801206491 chr15 102531392 6085507 0.059352622463176935 0.32079088279147466 chr16 90354753 5364709 0.05937384389728784 0.41433554441599324 chr17 81195210 4827795 0.059459110950017866 0.33890474440186996 chr18 78077248 6229847 0.07979081178680889 1.3905271877602916 chr19 59128983 4178851 0.07067348004277361 0.8604179726350326 chr20 63025520 3752668 0.059542039478611204 0.35794146782215003 chr21 48129895 4528237 0.09408366671067951 0.49967415419769434 chr22 51304566 1977109 0.03853670646000592 0.25636681669701167 chrMT 16571 105874 6.389113511556333 4.370202874661337 chrX 155270560 7299527 0.047011661450824936 0.34686325836330517 chrY 59373566 534616 0.009004276414861118 0.2045088978880566