序列分析常规设置

RUNNUMBER1(04/04/15atProjectinformation: = =DNAGenotypicData=0SettingsusedforGeneralsettingsDeletionWeight缺失 =1TransitionWeightWeight重复 =1TranversionWeightWeight颠换 =1EpsilonValue =1e-07Significantdigitsforoutput=5UseoriginalhaplotypedefinitionAlllowedlevelofmissingdata=0.05ActiveStandardMolecularDiversityMolecularDistance:Pairwisedifference AValue 分子距离配对差异=0.05Thetaestimators Printoutinter-haplotypicdistancematrixHaplotypicFrequencyestimation:Makeestimationsat148149 152163164 167178179 182193194 197208209 212223224 227238239 242253254 257268269 272283284 287298299 302313314 317328329 332343344 347358359 362373374 377388389 392403404 407418419 422433434 437448449 452463464 467478479 482493494 497508509 512523524Listoflociwithtoomuchmissingdata===Checkingforhaplotypessharedamong=Population种群HaplotypessharedbetweenS1andS1":单倍型“S1”和“S1”之间共Da-1=Da-2Da-1=Da-3Da-1=Da-4Da-2=Da-3Da-2=Da-4Da-3=Da-4Da-5=Da-6Da-5=Da-7Da-5=Da-8Da-5=Da-9Da-5=Da-10Da-6=Da-7Da-6=Da-8Da-6=Da-9Da-6=Da-10Da-7=Da-8Da-7=Da-9Da-7=Da-10Da-8=Da-9Da-8=Da-10Da-9=Da-HaplotypessharedbetweenS1andS2":单倍型“S1”和“S2”之间共Da-1=S-13Da-1=S-14Da-1=S-15Da-1=S-16Da-1=S-17Da-1=S-18Da-1=S-19Da-1=S-20Da-2=S-13Da-2=S-14Da-2=S-15Da-2=S-16Da-2=S-17Da-2=S-18Da-2=S-19Da-2=S-20Da-3=S-13Da-3=S-14Da-3=S-15Da-3=S-16Da-3=S-17Da-3=S-18Da-3=S-19Da-3=S-20Da-4=S-13Da-4=S-14Da-4=S-15Da-4=S-16Da-4=S-17Da-4=S-18Da-4=S-19Da-4=S-HaplotypessharedbetweenS1andG1":单倍型“S1”和“G1”之间共Da-1=G-21Da-2=G-21Da-3=G-21Da-4=G-==Population:HaplotypessharedbetweenS2andS1":单倍型“S2”和“S1”之间共S-13=Da-1S-13=Da-2S-13=Da-3S-13=Da-4S-14=Da-1S-14=Da-2S-14=Da-3S-14=Da-4S-15=Da-1S-15=Da-2S-15=Da-3S-15=Da-4S-16=Da-1S-16=Da-2S-16=Da-3S-16=Da-4S-17=Da-1S-17=Da-2S-17=Da-3S-17=Da-4S-18=Da-1S-18=Da-2S-18=Da-3S-18=Da-4S-19=Da-1S-19=Da-2S-19=Da-3S-19=Da-4S-20=Da-1S-20=Da-2S-20=Da-3S-20=Da-HaplotypessharedbetweenS2andS2":单倍型“S2”和“S2”之间共S-13=S-14S-13=S-15S-13=S-16S-13=S-17S-13=S-18S-13=S-S-13=S-20S-14=S-15S-14=S-16S-14=S-17S-14=S-18S-14=S-19S-14=S-20S-15=S-16S-15=S-17S-15=S-18S-15=S-19S-15=S-20S-16=S-17S-16=S-18S-16=S-19S-16=S-20S-17=S-18S-17=S-19S-17=S-20S-18=S-19S-18=S-20S-19=S-HaplotypessharedbetweenS2andG1":单倍型“S2”和“G1享S-13=G-21S-14=G-21S-15=G-21S-16=G-21S-17=G-21S-18=G-21S-19=G-21S-20=G-==Population:Haplotypessharedbetween"G1"andG-21=Da-1G-21=Da-2G-21=Da-3G-21=Da-Haplotypessharedbetween"G1"andG-21=S-13G-21=S-14G-21=S-15G-21=S-16G-21=S-17G-21=S-18G-21=S-19G-21=S-Haplotypessharedbetween"G1"and"G1":G-2=G-18G-2=G-G-2=G-12G-2=G-11G-18=G-25G-18=G-12G-18=G-11G-25=G-12G-25=G-11G-12=G-==Population:Haplotypessharedbetween"G2"and"G2":G5=G6G5=G8G5=G9G5=G11G6=G8G6=G9G6=G11G8=G9G8=G11G9=Haplotypefrequencydistributionamongthesamples样品中单倍型频率HaplotypeHaplotype HaplotypeHaplotypefrequenciesinpopulations (10)(10)481060000100010000500010001000100010000100010001000100050001Relativefrequencies (10)(10)0000000000000000000000000000000000000000000GENETIC Numberofusablelocifordistancecomputation:603Allowedlevelofmissingdata :0.05Listofusableloci 148149 152163164 167178179 182193194 197208209 212223224 227238239 242253254 257268269 272283284 287298299 302313314 317328329 332343344 347358359 362373374 377388389 392403404 407418419 422433434 437448449 452463464 467478479 482493494 497508509 512523524ListoflociwithtoomuchmissingdataAMOVAYSISGeneticstructuretotestNo.ofGroups=StructureName="mtDNAsequencesinthePenaeusVanmamei"NbGroups=1IndividualLevel=0Distel=""}DistancemethodPairwisedifferenceAMOVAdesignandresultsAMOVAReference:Weir,B.S.andCockerham,C.C.Excoffier,L.,Smouse,P.,andQuattro,J.1992.Weir,B.S.,1996.SourceofSumofof FixationIndex固定指 FST PopulationspecificFSTindices种群具体FST指数 12341234VaandFST:P(rand.value>obs.value)=0.00000P(rand.value=obs.value)=0.00000P-value=0.00000+-ComparisonsofpairsofpopulationsamplesListoflabelsforpopulationsamplesused Population PopulationaveragepairwisedifferencesAbovediagonal对角线上方 :Averagenumberofpairwisedifferencesbetweenpopulations(PiXY)种群之间的成对差异平均数（PIXY）DiagonalelementsAveragenumberofpairwisedifferenceswithinpopulation(PiX)对角线元素：种群内成对差异平均数（PIX）Belowdiagonal CorrectedaveragepairwisedifferencePiXY-(PiX+PiY)/2)下面对角线：修正平均配对差异（PiXY-（PIX+PIY）/2）DistancemethodPairwisedifference12341234PXYP123234CorrectedPXYP 34==YSESATTHEINTRA-POPULATION==Sample:Standarddiversityindices标准的多样性指数Reference:Nei,M.,No.ofgenecopies :10No.ofsequences :10No.ofloci数 :603No.ofusableloci 可用数 :603lociwithlessthan5.00%missingdataNoofpolymorphicsites多态位点的数目Resultsareonlyshownforpolymorphicloci Haplotype-levelcomputationsSumofsquarefreqs频率平方总和 :Genediversity多样 :1.0000+/-(Standarddeviationisforthesamplingprocess采样过程的标准偏差Moleculardiversityindices分子多样性指数Reference:Tajima,F.,Tajima,F.Nei,M.,Zouros,E.,Ewens,W.J.SampleNo.of::Deletion:Transition:Transversion:Allowedlevelofmissing:5.0000Numberofobservedtransitions观测到转换数 :0Numberofobservedtransversions颠换数 :1Numberofsubstitutions替换 :1Numberofobservedindels插入和缺失 :0Numberofpolymorphicsites多态位点 :1Numberofobservedsiteswithtransitions转换位点 :0Numberofobservedsiteswithtransversions:1Numberofobservedsiteswithsubstitutions:1Numberofobservedsiteswithindels :0Numberofobservednucleotidesites :603Numberofusablenucleotide :Nucleotidecomposition核苷酸组成(Relativevalues)C:10.28%T:A:G:TotalDistancemethod :Pairwisedifference(Gcorrection:a=0.05)Inter-haplotypicdistancematrix(s.d.above 0.99920.9992 0.9992 Da-4 0.00000.99920.9992 Da-5 1.00000.00000.0000 Da-6 1.00000.00000.0000 Da-7 1.00000.00000.0000Da-8 1.0000 0.0000Da-9 1.00000.0000 Da-101.00001.00000.00000.0000ListofDa-1:Da-2:Da-3:Da-4:Da-5:Da-6:Da-7:Da-8:Da-9:Da-10:Meannumberofpairwisedifferences平均成对差异数量 Nucleotidediversity(averageoverloci)核苷酸多态性（平均超过 0.000884+/- (Standarddeviationsareforboththesamplingandthestochasticprocesses)标准偏差为采样和随机过程UnabletocomputeTheta(Homwhenallgenecopiesaredifferent无UnabletocomputeTheta(k)whenallgenecopiesaredifferentTheta(S): S.D.Theta(S) Theta(Pi) S.D.Theta(Pi) Haplotypesfrequencyestimation单倍型频率估算Reference:Dempster,A.,N.LairdandD.Rubin,Excoffier,L.andM.Slatkin.1995.Lange,K.,1997.Weir,B.S.,Excoffier,L.,Laval,G.,andBalding,Haplotypedatabasecontent单倍型数据库内容: 10.40000020.600000Tajima'stestofselectiveneutrality选择中性的田岛的测试Reference:Tajima,F.Tajima,F.,Sample 样本 No.ofsiteswithsubstitutions位点的取代量(S) MeanNo.ofpairwisedifferences平均成对差异量(Pi):0.53333Distancemethod :Pairwisedifference配对差异(noGcorrection,indelsnottakenintoaccount)Tajima's :No.of Obs. :Mean :S.D. :Mean :-S.D. :P(Dsimul<D :==Fu'sFstestofselectiveneutrality:Reference:Fu,Y.X.OriginalNo.ofalleles(k) Exp.No.of :-No.of Mean S.D. Mean S.D. Prob(sim_Fs ==Sample:==Standarddiversityindices:Reference:Nei,M.,No.ofgene :No.of :No.of :No.ofusableloci :603lociwithlessthan5.00%missingNo.ofpolymorphicsites:Resultsareonlyshownforpolymorphicloci2222Haplotype-levelSumofsquare :Genediversity :1.0000+/-0.0447(Standarddeviationisforthesamplingprocess)==Moleculardiversityindices:Reference:Tajima,F.,Tajima,F.Nei,M.,Zouros,E.,Ewens,W.J.Sample :No.of :Deletion :Transition :Transversionweight :1.0000Allowedlevelofmissingdata :5.0000%Numberofobserved :Numberofobserved :Numberof :Numberofobserved :Numberofpolymorphicsites :4Numberofobservedsiteswithtransitions :2Numberofobservedsiteswithtransversions:2Numberofobservedsiteswithsubstitutions:4Numberofobservedsiteswithindels :0Numberofobservednucleotidesites :603Numberofusablenucleotide :Nucleotidecomposition(Relativevalues)C:10.32%T:A:G:TotalDistancemethod :Pairwisedifference(Gcorrection:a=0.05)Inter-haplotypicdistancematrix(s.d.aboveS- 1.72771.00000.00001.00000.00001.00000.00001.00000.00001.00000.00001.00001.00001.0000List:Meannumberofpairwisedifferences 0.800000Nucleotidediversity(averageoverloci) 0.001327(StandarddeviationsareforboththesamplingandthestochasticUnabletocomputeTheta(Hom)whenallgenecopiesaredifferentUnabletocomputeTheta(k)whenallgenecopiesaredifferentTheta(S) S.D.Theta(S) Theta(Pi) S.D.Theta(Pi) ==Haplotypesfrequencyestimation:Reference:Dempster,A.,N.LairdandD.Rubin,Excoffier,L.andM.Slatkin.1995.Lange,K.,1997.Weir,B.S.,Excoffier,L.,Laval,G.,andBalding,Haplotypedatabase 10.10000020.10000030.800000==Tajima'stestofselectiveneutrality:Reference:Tajima,F.Tajima,F.,Sample No.ofsiteswithsubstitutions(S) MeanNo.ofpairwisedifferences(Pi):Distancemethod :Pairwisedifference(noGcorrection,indelsnottakenintoaccount)Tajima's :-No.of Obs. Mean S.D. Mean :-S.D. :P(Dsimul<D :==Fu'sFstestofselectiveneutrality:Reference:Fu,Y.X.OriginalNo.ofalleles(k) Exp.No.of -No.of Mean S.D. Mean S.D. Prob(sim_Fs ==Sample:==Standarddiversityindices:Reference:Nei,M.,No.ofgene :No.of :No.of :No.ofusableloci :603lociwithlessthan5.00%missingNo.ofpolymorphicsites:Resultsareonlyshownforpolymorphic222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222Haplotype-levelSumofsquare :Genediversity :1.0000+/-0.0447(Standarddeviationisforthesamplingprocess)==Moleculardiversityindices:Reference:Tajima,F.,Tajima,F.Nei,M.,Zouros,E.,Ewens,W.J.Sample :No.of :Deletion :Transition :Transversionweight :1.0000Allowedlevelofmissingdata :5.0000%Numberofobserved :Numberofobserved :Numberof :Numberofobserved :Numberofpolymorphicsites :90Numberofobservedsiteswithtransitions :63Numberofobservedsiteswithtransversions:26Numberofobservedsiteswithsubstitutions:89Numberofobservedsiteswithindels :1Numberofobservednucleotidesites :603Numberofusablenucleotide :Nucleotidecomposition(Relativevalues)C:10.33%T:A:G:TotalDistancemethod :Pairwisedifference(Gcorrection:a=0.05)Inter-haplotypicdistancematrix(s.d.above G-3G-0.0000G-180.00000.9992G-250.00000.00000.9992G-2189.00008.66938.71008.6693G-141.00001.00000.99921.4119G-138.00008.00002.80962.6303G-120.00000.00001.00000.00000.9992G-110.00000.00001.00000.9992G-31.00001.00002.0000 G-12.00002.00002.000089.00003.00006.00002.0000ListofHaplotypes:G-2:G-18:G-25:G-21:G-14:G-13:G-12:G-11:G-3:G-1:Meannumberofpairwisedifferences 19.577778+/-Nucleotidediversity(averageoverloci) 0.032467+/-(StandarddeviationsareforboththesamplingandthestochasticUnabletocomputeTheta(Hom)whenallgenecopiesaredifferentUnabletocomputeTheta(k)whenallgenecopiesaredifferentTheta(S) S.D.Theta(S) Theta(Pi) S.D.Theta(Pi) ==Haplotypesfrequencyestimation:Reference:Dempster,A.,N.LairdandD.Rubin,Excoffier,L.andM.Slatkin.1995.Lange,K.,1997.Weir,B.S.,Excoffier,L.,Laval,G.,andBalding,Haplotypedatabase 10.50000020.100000 30.10000040.10000050.10000060.100000==Tajima'stestofselectiveneutrality:Reference:Tajima,F.Tajima,F.,Sample No.ofsiteswithsubstitutions(S) MeanNo.ofpairwisedifferences(Pi):Distancemethod :Pairwisedifference(noGcorrection,indelsnottakenintoaccount)Tajima's :-No.of Obs.:Mean:S.D.:Mean:-S.D.:P(Dsimul<D :==Fu'sFstestofselectiveneutrality:Reference:Fu,Y.X.OriginalNo.ofalleles(k) Exp.No.ofalleles No.of Mean S.D. Mean S.D. Prob(sim_Fs ==Sample:==Standarddiversityindices:Reference:Nei,M.,No.ofgene :No.of :No.of :No.ofusableloci :603lociwithlessthan5.00%missingNo.ofpolymorphicsites:Resultsareonlyshownforpolymorphic22222222222222222222222222Haplotype-levelSumofsquare :Genediversity :1.0000+/-0.0447(Standarddeviationisforthesamplingprocess)==Moleculardiversityindices:Reference:Tajima,F.,Tajima,F.Nei,M.,Zouros,E.,Ewens,W.J.Sample :No.of :Deletion :Transition :Transversionweight :1.0000Allowedlevelofmissingdata :5.0000%Numberofobserved :Numberofobservedtransversions :10Numberofsubstitutions :25Numberofobserved :Numberofpolymorphicsites :26Numberofobservedsiteswithtransitions :15Numberofobservedsiteswithtransversions:10Numberofobservedsiteswithsubstitutions:25Numberofobservedsiteswithindels :1Numberofobservednucleotidesites :603Numberofusablenucleotidesites :603Nucleotidecomposition(Relativevalues)C:10.18%T:A:G:TotalDistancemethod :Pairwisedifference(Gcorrection:a=0.05)Inter-haplotypicdistancematrix(s.d.above 4.5021G24.70354.7035G321.00001.41191.4119G43.00003.0000 4.80054.80054.80054.8005G521.00000.00000.0000G621.00000.00000.0000G722.00000.99920.9992G821.00000.0000G921.0000 G1121.000023.00002.000024.00000.00000.00000.0000ListofHaplotypes:G1:G2:G3:G4:G5:G6:G7:G8:G9:G11:Meannumberofpairwisedifferences 11.177778+/-Nucleotidediversity(averageoverloci) 0.018537+/-(StandarddeviationsareforboththesamplingandthestochasticUnabletocomputeTheta(Hom)whenallgenecopiesaredifferentUnabletocomputeTheta(k)whenallgenecopiesaredifferentTheta(S) S.D.Theta(S) Theta(Pi) S.D.Theta(Pi) ==Haplotypesfrequencyestimation:Reference:Dempster,A.,N.LairdandD.Rubin,Excoffier,L.andM.Slatkin.1995.Lange,K.,1997.Weir,B.S.,Excoffier,L.,Laval,G.,andBalding,Haplotypedatabase 10.10000020.10000030.10000040.10000050.50000060.100000==Tajima'stestofselectiveneutrality:Reference:Tajima,F.Tajima,F.,Sample No.ofsiteswithsubstitutions(S) MeanNo.ofpairwisedifferences(Pi):Distancemethod :Pairwisedifference(noGcorrection,indelsnottakenintoaccount)Tajima's :No.of Obs.:Mean:S.D.:Mean:-S.D.:P(Dsimul<D :==Fu'sFstestofselectiveneutrality:Reference:Fu,Y.X.OriginalNo.ofalleles(k) Exp.No.ofalleles No.of Mean S.D. Mean S.D. Prob(sim_Fs ==SummaryofcomputationsdonewithinBasic No.ofgene No.of No.ofusable No.ofpolym.14 ExpectedTot.123456789 Numberofs.d.11111121111131111141111151111161111171111181111191111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111121211111111111111111111111111111111111111111111111111111111111111111112221111111111122121111111111111111111111111111111111111111111111111111111122121111111111111111111111111111111111111111111111111111212112221111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111221211111111111111111212112121121211212122121111111222111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112121111111111111111121211212112121111111212111111111111111112121111111212111111121211111111111111111111111111111111212111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112121111111111111111111111111111111111111111111111111111111111111111111111111111111111212111111111111111111111111111222111111111111111111111111111212111111111111111111111111111111111111111111111111111111111111111111111111111111111111111222111111111111111112121111111111111111111111111111111111111111111111111111111112121111111111111111111111111111111111111111111111111111111111111111111212112121111111223112121111111111111111111111212111111111111111111111111111111111111111111111111111111111212112121111111212111111121211111112121111