BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081123.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 = 2,284,892 number of mapped reads = 2,134,043 (93.4%) number of supplementary alignments = 12,783 (0.56%) number of secondary alignments = 0 number of mapped bases = 145,712,860 bp number of sequenced bases = 145,655,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,390 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1424 >>>>>>> ACTG content number of A's = 40,869,392 bp (28.06%) number of C's = 28,159,075 bp (19.33%) number of T's = 44,840,831 bp (30.79%) number of G's = 31,784,885 bp (21.82%) number of N's = 1,628 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,279,930 number of insertions = 11,153 mapped reads with insertion percentage = 0.52% number of deletions = 31,580 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.4198X There is a 3.94% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 13656879 0.054791755162768484 0.5661392782844987 chr2 243199373 10309761 0.04239221866743875 0.48180747803548696 chr3 198022430 12045093 0.06082691238563227 0.2883684637110341 chr4 191154276 9411713 0.049236214836229975 0.29843080044356207 chr5 180915260 9175625 0.0507178056732196 0.2621100164079394 chr6 171115067 11997458 0.07011339334601084 0.4630582067141951 chr7 159138663 6437011 0.040449070506517956 0.43249305552022727 chr8 146364022 9861154 0.06737416658309649 0.4369340379949908 chr9 141213431 8290129 0.05870637758245531 0.6338834824893029 chr10 135534747 6362514 0.046943784828845404 0.43508518081989966 chr11 135006516 6408152 0.04746550159104913 0.3448862266799182 chr12 133851895 6128055 0.04578235519190819 0.2791640800573796 chr13 115169878 3616847 0.031404452820554346 0.20041044963107107 chr14 107349540 4449501 0.041448719761631024 0.35637474467298474 chr15 102531392 3310826 0.032290851956832886 0.21341063289125323 chr16 90354753 4103668 0.04541728977998534 0.37041516184452233 chr17 81195210 3310170 0.04076804530710617 0.24520659240143153 chr18 78077248 3752191 0.04805741872459439 1.0256189005928824 chr19 59128983 2867515 0.04849592965263752 0.48030776461107977 chr20 63025520 2665042 0.042285125136611326 0.25727473568910975 chr21 48129895 1544556 0.03209140597543377 0.3610377524417966 chr22 51304566 1440235 0.028072257740178526 0.18936057492051 chrMT 16571 83886 5.062217126304991 3.684376712754061 chrX 155270560 4084302 0.026304419846234856 0.2328785844306244 chrY 59373566 400577 0.0067467229440118185 0.1975586448336024