forked from GRIAC/system_genetics
This is a test
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---
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title: "Sample workflow DESeq2 for Tessa"
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author: "Corneel Vermeulen"
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date: "`r Sys.Date()`"
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output: html_document
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---
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### GSK asthma remission project
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Hoi Tesssa, Dit is een aangepaste versie van het tutorial script dat ik voor Ilse maakte, vanwege een [verandering in DESeq2 VERSION 1.16.0](# https://support.bioconductor.org/p/95695/). Omdat de orginele count table erg groot is gebruikt het script een miniatuur versie gemaakt van 1000 willekeurige features.
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### Preliminaries
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load all required packages
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```{r load_packgs, warning=FALSE, message=FALSE}
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library("DESeq2")
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library("gplots")
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```
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### load data
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Hier laad je de count table and de database respectievelijk. Je kunt hier evt. je werkmap instellen.
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```{r setwd_dataload}
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#setwd("/path/to/your/wd")
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CT<-read.delim("sample.htseq.txt.table", header = TRUE, sep = "\t",
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quote = "", fill = TRUE, comment.char = "")
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db <-read.csv("db.csv",header=T,sep=";",dec=",")
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```
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### Prepare data
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Dit is het lastigste stuk. De sample_IDs zijn gemangeld tijdens het verwerken van de samples en dat maakt het matchen aan de klinische data een tijdrovende klus.
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```{r showids}
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head(colnames(CT))
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head(db$rnaseq.id)
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```
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Ik heb al wat werk verzet door in de db overal een "X" voor te plakken en alle streepjes te vervangen door underscores. Nu moeten we nog de ".htseq.txt" kwijtraken. Zie ook dat sommige samples "NORM" en anderen "NORM_" genoemd zijn. Verder zijn er meerdere controle samples. Veel lelijke code hier, en waarschijnlijk niet bruikbaar voor jou:
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```{r prepdata}
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colnames(CT)[1] <- ""
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cn.CT <- colnames(CT)
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cn.CT <- cn.CT[2:length(cn.CT)] #drop the empty first cell
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cn.CT <- gsub(".htseq.txt", "", cn.CT) # remove the suffix
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cn.CT <- gsub("NORM.{0,}", "NORM_", cn.CT) # add one trailing underscore
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cn.all <- as.character(db$rnaseq.id)
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idx <- match(cn.CT,cn.all) #match the clinical data to the correct samples
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idx[which(is.na(idx))] <- which(cn.all == "X263_110_T04_90226") # multiple ref samples
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coldata <- db[idx,]
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rownames(coldata) <- cn.CT
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countdata <- CT[,c(2:ncol(CT))]
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rownames(countdata) <- CT[,1]
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coldata$batch.extract[which(coldata$rnaseq.id == "X263_110_T04_90226")] <- seq(1:6)
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coldata$batch.extract<-as.factor(coldata$batch.extract) #batch nrs are factor levels
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```
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### QC-filter
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We gebruiken alleen samples die de QC doorstaan en de beste reference sample (#2).
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```{r qcfilter, message=FALSE}
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qc.pass <- scan("rnaseqids_qc4_pass_plusref2.txt", what = "character")
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idx.qc.pass <- which(coldata$rnaseq.id %in% qc.pass)
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idx.ref2 <- which(coldata$rnaseq.id == "X263_110_T04_90226" & coldata$batch.extract == 2)
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idx.qc.pass <- c(idx.qc.pass,idx.ref2)
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coldata <- coldata[idx.qc.pass,]
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countdata <- countdata[,idx.qc.pass]
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colnames(countdata) <- NULL # fixes error
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```
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### Exploratory analysis
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Nu we onze data klaar hebben, wordt alles veel eenvoudiger: We converteren onze count table naar een DESeqDataSet. We geven nog geen model op.
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```{r convert}
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dds <- DESeqDataSetFromMatrix(countData = countdata,
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colData = coldata,
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design = ~ 1)
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```
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Dan kijken we in een PCA of onze dataset zich gedraagt. Het is noodzakelijk de ruwe count data te transformeren daarvoor. Omdat we teveel samples hebben om een rlog transformatie te doen gebruiken we een [trucje](https://support.bioconductor.org/p/77122/).
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```{r pca, message = FALSE}
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dds <- estimateSizeFactors(dds)
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baseMean <- rowMeans(counts(dds, normalized=TRUE))
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idx.sub <- sample(which(baseMean > 5), 100)
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dds.sub <- dds[idx.sub, ]
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dds.sub <- estimateDispersions(dds.sub)
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dispersionFunction(dds) <- dispersionFunction(dds.sub)
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vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
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plotPCA(vsd, intgroup = "gender")
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```
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### Differential expression
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Tenslotte het echte werk. We voeren ons model in en creeren een nieuwe DESeqDataSet (de oude wordt daarbij overschreven). Dan testen we of er een overall verschil is tussen de levels van asthma. Vervolgens kijken we naar een specifiek contrast.
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```{r difexp, message = FALSE}
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dds <- DESeqDataSetFromMatrix(countData = countdata,
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colData = coldata,
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design = ~ gender + asthma.ics)
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# Overall test (takes long time to run)
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dds <- DESeq(dds, test="LRT", full=~ gender + asthma.ics, reduced=~ gender)
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res <- results(dds)
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res$symbol <- mcols(dds)$symbol
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head(res[order(res$pvalue),],4)
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summary(res)
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sum(res$padj < 0.05, na.rm=T)
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topGene <- rownames(res)[which.min(res$padj)]
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plotCounts(dds, gene=topGene, intgroup=c("asthma.ics"))
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```
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Het feature met de meeste variatie tussen de groepen is `r topGene`, maar waarschijnlijk ben je geinteresseerd in een specifiek contrast, bijvoorbeeld asthma versus healthy:
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```{r contrast}
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dds.wald <- DESeq(dds, test="Wald", betaPrior = TRUE)
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res.c <- results(dds.wald, contrast = c("asthma.ics","PersA_no_ICS","H"))
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topGene.c <- rownames(res.c)[which.min(res.c$padj)]
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```
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Het feature dat het meest verschillend tot expressie komt in dit contrast is `r topGene.c`. Hierna zul je zelf je weg moeten vinden. Meer informatie vind je [hier](http://www.bioconductor.org/help/workflows/rnaseqGene/) en [hier](https://www.bioconductor.org/help/course-materials/2015/LearnBioconductorFeb2015/B02.1.1_RNASeqLab.html).
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## session info
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Packages used
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```{r sessionInfo, include=TRUE, echo=TRUE, results='markup'}
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sessionInfo()
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```
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"rnaseq.id";"batch.extract";"gender";"asthma.ics";"age";"currentsmoking"
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"X9_0_T06_90304";1;"male";"PersA_ICS";48,29021;"nonsmoker"
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"X613_0_T07_90064";1;"female";"PersA_ICS";53,6783;"nonsmoker"
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"X377_0_T06_90091";1;"male";"PersA_ICS";67,27995;"nonsmoker"
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"X535_0_T07_90052";2;"female";"PersA_ICS";37,57974;"nonsmoker"
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"X433_0_T06_90135";2;"female";"PersA_ICS";50,78702;"nonsmoker"
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"X25_0_T06_90258";2;"female";"PersA_ICS";45,77949;"nonsmoker"
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"X504_0_T07_90051";2;"male";"ClinR";52,11773;"nonsmoker"
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"X545_0_T07_90061";2;"female";"PersA_ICS";36,43806;"nonsmoker"
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"X440_0_T06_90072";3;"female";"PersA_no_ICS";55,91239;"nonsmoker"
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"X615_0_T06_90136";3;"male";"PersA_ICS";39,42505;"nonsmoker"
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"X1406_0_T04_90217";3;"female";"ClinR";63,5373;"smoker"
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"X527_0_T07_90029";3;"male";"ClinR";45,21287;"nonsmoker"
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"X451_0_T06_90027";4;"male";"PersA_ICS";39,8987;"nonsmoker"
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"X543_0_T06_90110";4;"male";"PersA_ICS";25,10609;"smoker"
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"X436_0_T06_90160";4;"male";"PersA_ICS";58,0916;"nonsmoker"
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"X699_0_T06_90067";4;"female";"PersA_no_ICS";27,38946;"nonsmoker"
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"X650_0_T06_90058";5;"female";"PersA_ICS";54,59001;"nonsmoker"
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"X1417_0_T06_90320";5;"female";"PersA_ICS";56,31485;"nonsmoker"
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"X636_0_T07_90028";5;"male";"PersA_no_ICS";52,3614;"smoker"
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"X1317_0_T03_90195";6;"female";"ComR";55,6029;"nonsmoker"
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"X434_0_T06_90088";6;"male";"PersA_ICS";36,01643;"smoker"
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"X1408_0_T04_90132";6;"female";"PersA_no_ICS";60,64351;"nonsmoker"
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"X70_0_T06_90296";6;"male";"ClinR";51,11567;"smoker"
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"X51_0_T06_90222";6;"male";"PersA_ICS";46,23397;"nonsmoker"
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"X1322_0_T04_90118";7;"male";"PersA_no_ICS";44,39687;"nonsmoker"
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"X1319_0_T03_90187";7;"female";"ComR";66,5762;"nonsmoker"
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"X454_0_T06_90220";7;"female";"PersA_ICS";50,48038;"nonsmoker"
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"X1503_0_T06_90169";7;"male";"PersA_no_ICS";49,46201;"smoker"
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"X67_0_T06_90307";7;"male";"PersA_no_ICS";52,45722;"smoker"
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"X66_0_T06_90281";7;"male";"PersA_no_ICS";50,14089;"smoker"
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"X1405_0_T04_90245";8;"male";"ClinR";65,5632;"nonsmoker"
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"X530_0_T07_90019";8;"male";"PersA_ICS";49,43737;"nonsmoker"
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"X1403_0_T04_90220";8;"male";"ClinR";60,54746;"nonsmoker"
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"X1320_0_T03_90210";8;"male";"ComR";67,54814;"nonsmoker"
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"X550_0_T07_90049";8;"male";"PersA_ICS";35,46886;"nonsmoker"
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"X662_0_T06_90096";9;"female";"PersA_ICS";40,282;"nonsmoker"
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"X450_0_T06_90202";9;"female";"ClinR";50,71857;"nonsmoker"
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"X721_0_T06_90219";9;"female";"PersA_ICS";28,93087;"smoker"
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"X464_0_T06_90221";9;"female";"PersA_ICS";54,56251;"nonsmoker"
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"X728_0_T06_90052";10;"male";"PersA_ICS";38,42026;"smoker"
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"X641_0_T06_90063";10;"male";"PersA_ICS";49,27858;"nonsmoker"
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"X423_0_T06_90237";10;"female";"PersA_ICS";33,01289;"smoker"
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"X33_0_T07_90020";10;"male";"PersA_ICS";50,26146;"nonsmoker"
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"X1323_0_T04_90114";11;"male";"ClinR";46,53514;"nonsmoker"
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"X496_0_T06_90319";11;"female";"PersA_ICS";30,31348;"nonsmoker"
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"X1327_0_T05_90074";12;"male";"PersA_no_ICS";46,46943;"nonsmoker"
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"X730_0_T06_90064";12;"female";"PersA_ICS";49,56879;"nonsmoker"
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"X518_0_T06_90188";12;"female";"PersA_ICS";38,98688;"smoker"
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"X466_0_T06_90045";12;"male";"PersA_no_ICS";38,90486;"nonsmoker"
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"X413_0_T06_90159";13;"female";"PersA_no_ICS";52,77744;"nonsmoker"
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"X460_0_T06_90266";13;"female";"PersA_ICS";28,62685;"nonsmoker"
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"X419_0_T06_90175";13;"female";"PersA_ICS";54,72952;"nonsmoker"
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"X642_0_T07_90030";13;"female";"ClinR";46,2204;"nonsmoker"
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"X749_0_T06_90080";13;"male";"PersA_ICS";46,89665;"nonsmoker"
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"X1502_0_T05_90096";14;"male";"PersA_no_ICS";63,83025;"nonsmoker"
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"X1404_0_T04_90182";15;"male";"PersA_no_ICS";47,21686;"nonsmoker"
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"X1504_0_T06_90174";15;"female";"PersA_ICS";53,50297;"nonsmoker"
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"X378_0_T06_90242";15;"male";"PersA_ICS";40,24903;"nonsmoker"
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"X1410_0_T05_90120";15;"male";"ComR";49,2593;"nonsmoker"
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"X13_0_T06_90295";16;"male";"PersA_ICS";52,12594;"nonsmoker"
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"X1402_0_T05_90007";16;"male";"PersA_ICS";59,44444;"smoker"
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"X304_0_T06_90224";17;"male";"PersA_no_ICS";50,74595;"smoker"
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"X1413_0_T07_90004";17;"female";"PersA_ICS";35,98905;"nonsmoker"
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"X658_0_T06_90150";17;"female";"PersA_no_ICS";35,15663;"nonsmoker"
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"X478_0_T06_90151";17;"female";"ClinR";41,07039;"nonsmoker"
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"X1401_0_T04_90183";17;"male";"ComR";64,92802;"smoker"
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"X1412_0_T06_90303";18;"female";"PersA_ICS";64,76397;"smoker"
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"X632_0_T07_90050";18;"female";"PersA_ICS";54,48871;"nonsmoker"
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"X353_0_T06_90035";18;"male";"PersA_ICS";51,76181;"nonsmoker"
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"X399_0_T06_90196";18;"female";"PersA_ICS";49,76306;"nonsmoker"
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"X1411_0_T06_90006";18;"female";"ClinR";58,63119;"smoker"
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"X1505_0_T07_90037";19;"female";"PersA_ICS";40,05202;"nonsmoker"
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"X742_0_T06_90069";19;"male";"PersA_ICS";35,04997;"nonsmoker"
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"X695_0_T06_90053";19;"female";"ComR";28,61054;"nonsmoker"
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"X391_0_T06_90238";20;"male";"PersA_ICS";59,41399;"nonsmoker"
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"X1415_0_T07_90003";20;"male";"PersA_ICS";53,70021;"nonsmoker"
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"X474_0_T06_90079";20;"female";"PersA_no_ICS";28,57495;"nonsmoker"
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"X487_1_T04_90142";18;"male";"PersA_no_ICS";38,65834;"nonsmoker"
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"X124_11_T05_90014";5;"male";"PersA_no_ICS";64,27116;"smoker"
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"X80_11_T04_90157";7;"female";"ClinR";71,6823;"nonsmoker"
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"X7_21_T04_90179";1;"female";"ClinR";42,68846;"nonsmoker"
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"X57_21_T05_90106";5;"male";"ClinR";47,85478;"nonsmoker"
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"X175_21_T05_90105";19;"female";"ClinR";60,01369;"nonsmoker"
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"X195_22_T04_90096";8;"male";"ClinR";40,93623;"nonsmoker"
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"X53_22_T04_90131";10;"male";"ClinR";38,84999;"nonsmoker"
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"X22_27_T04_90144";13;"female";"ClinR";45,59879;"nonsmoker"
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"X108_110_T05_90051";1;"male";"ComR";51,54552;"smoker"
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"X98_110_T02_10430";1;"male";"ClinR";63,19496;"nonsmoker"
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"X77_110_T05_90091";2;"male";"PersA_ICS";67,51255;"nonsmoker"
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"X154_110_T05_90071";2;"male";"PersA_ICS";56,34486;"nonsmoker"
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"X37_110_T06_90046";3;"female";"PersA_ICS";71,83288;"nonsmoker"
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"X99_110_T05_90056";4;"female";"PersA_ICS";60,25724;"nonsmoker"
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"X54_110_T05_90052";4;"male";"PersA_no_ICS";53,10598;"smoker"
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"X33_110_T02_12543";4;"male";"PersA_no_ICS";48,3914;"nonsmoker"
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"X107_110_T05_90025";5;"female";"PersA_ICS";49,56046;"nonsmoker"
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"X111_110_T02_11651";5;"male";"ClinR";49,42083;"nonsmoker"
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"X87_110_T06_90007";5;"female";"PersA_no_ICS";57,41832;"smoker"
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"X112_110_T02_12285";6;"female";"ClinR";64,83767;"nonsmoker"
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"X45_110_T02_10969";8;"female";"PersA_no_ICS";62,70214;"nonsmoker"
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"X263_110_T04_90226";9;"male";"ComR";47,5235;"smoker"
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"X181_110_T06_90019";9;"male";"PersA_ICS";61,94114;"nonsmoker"
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"X132_110_T06_90009";11;"female";"PersA_ICS";61,55521;"nonsmoker"
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"X50_110_T02_09087";11;"female";"ClinR";60,87064;"nonsmoker"
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||||||
|
"X142_110_T06_90144";12;"male";"PersA_ICS";62,69667;"nonsmoker"
|
||||||
|
"X76_110_T02_09747";12;"female";"ComR";53,79055;"nonsmoker"
|
||||||
|
"X3_110_T05_90001";12;"female";"PersA_ICS";67,90965;"nonsmoker"
|
||||||
|
"X18_110_T05_90100";14;"male";"PersA_ICS";68,86505;"nonsmoker"
|
||||||
|
"X216_110_T03_90106";14;"male";"PersA_no_ICS";54,20112;"nonsmoker"
|
||||||
|
"X220_110_T04_90021";14;"male";"PersA_no_ICS";56,39995;"nonsmoker"
|
||||||
|
"X156_110_T05_90018";15;"male";"PersA_no_ICS";53,05407;"nonsmoker"
|
||||||
|
"X205_110_T04_90200";15;"male";"ClinR";51,37292;"nonsmoker"
|
||||||
|
"X183_110_T05_90090";15;"male";"PersA_ICS";50,08339;"nonsmoker"
|
||||||
|
"X176_110_T04_90246";16;"male";"ClinR";47,34018;"nonsmoker"
|
||||||
|
"X134_110_T04_90117";16;"female";"ClinR";57,44;"nonsmoker"
|
||||||
|
"X165_110_T05_90099";16;"male";"ClinR";58,34371;"smoker"
|
||||||
|
"X247_110_T02_07964";17;"male";"ComR";53,58236;"nonsmoker"
|
||||||
|
"X43_110_T05_90008";19;"female";"PersA_ICS";60,62434;"nonsmoker"
|
||||||
|
"X46_110_T05_90118";19;"female";"PersA_no_ICS";53,8152;"smoker"
|
||||||
|
"X9_210_T05_90023";1;"female";"ComR";48,95003;"nonsmoker"
|
||||||
|
"X201_210_T04_90113";3;"female";"ComR";48,98551;"nonsmoker"
|
||||||
|
"X107_210_T05_90026";3;"female";"PersA_ICS";23,05533;"nonsmoker"
|
||||||
|
"X60_210_T06_90065";6;"female";"ClinR";25,41832;"smoker"
|
||||||
|
"X108_210_T05_90062";9;"female";"ClinR";25,96566;"nonsmoker"
|
||||||
|
"X189_210_T05_90054";15;"female";"PersA_no_ICS";29,55499;"nonsmoker"
|
||||||
|
"X133_210_T05_90109";18;"female";"PersA_no_ICS";30,4011;"nonsmoker"
|
||||||
|
"X175_210_T06_90034";18;"male";"ClinR";61,58259;"nonsmoker"
|
||||||
|
"X23_220_T05_90086";9;"male";"PersA_no_ICS";35,41125;"smoker"
|
||||||
|
"X133_220_T05_90110";10;"male";"ClinR";27,50171;"nonsmoker"
|
||||||
|
"X135_220_T04_90135";10;"female";"ClinR";46,13541;"nonsmoker"
|
||||||
|
"X149_220_T04_90146";14;"male";"ClinR";37,74663;"nonsmoker"
|
||||||
|
"X67_220_T05_90072";16;"female";"PersA_no_ICS";26,54609;"nonsmoker"
|
||||||
|
"X99_220_T05_90057";16;"female";"ComR";33,21275;"nonsmoker"
|
||||||
|
"X154_230_T05_90116";13;"male";"PersA_no_ICS";21,59902;"smoker"
|
||||||
|
"X195_311_T06_90020";11;"male";"ComR";19,71538;"smoker"
|
||||||
|
"X201_311_T06_90280";14;"female";"PersA_ICS";20,55841;"nonsmoker"
|
||||||
|
"X175_311_T05_90103";16;"female";"ClinR";25,77128;"nonsmoker"
|
||||||
|
"X172_311_T05_90061";19;"female";"PersA_no_ICS";22,40372;"smoker"
|
||||||
|
"X37_331_T05_90019";13;"female";"ComR";18,17112;"nonsmoker"
|
||||||
|
"X37_NORM_";1;"female";"H";20,11761;"nonsmoker"
|
||||||
|
"X84_NORM_";1;"male";"H";24,26831;"smoker"
|
||||||
|
"X71_NORM_";1;"female";"H";70,80071;"nonsmoker"
|
||||||
|
"X6_NORM_";1;"female";"H";51,05807;"smoker"
|
||||||
|
"X102_NORM_";1;"female";"H";20,38866;"smoker"
|
||||||
|
"X81_NORM_";2;"female";"H";37,17728;"nonsmoker"
|
||||||
|
"X111_NORM_";2;"male";"H";20,32569;"smoker"
|
||||||
|
"X30_NORM_";2;"male";"H";63,52373;"nonsmoker"
|
||||||
|
"X128_NORM_";2;"male";"H";45,20465;"smoker"
|
||||||
|
"X25_NORM_";2;"male";"H";19,3128;"nonsmoker"
|
||||||
|
"X163_NORM_";3;"male";"H";21,64556;"nonsmoker"
|
||||||
|
"X159_NORM_";3;"male";"H";27,44159;"smoker"
|
||||||
|
"X24_NORM_";3;"male";"H";70,4449;"nonsmoker"
|
||||||
|
"X47_NORM_";3;"male";"H";66,8501;"nonsmoker"
|
||||||
|
"X78_NORM_";3;"female";"H";19,89585;"nonsmoker"
|
||||||
|
"X85_NORM_";4;"male";"H";28,65423;"smoker"
|
||||||
|
"X122_NORM_";4;"male";"H";57,52213;"smoker"
|
||||||
|
"X39_NORM_";4;"female";"H";21,58784;"nonsmoker"
|
||||||
|
"X4_NORM_";4;"male";"H";73,03206;"nonsmoker"
|
||||||
|
"X28_NORM_";4;"male";"H";49,58236;"smoker"
|
||||||
|
"X46_NORM_";5;"female";"H";23,63028;"nonsmoker"
|
||||||
|
"X108_NORM_";5;"male";"H";19,77276;"smoker"
|
||||||
|
"X99_NORM_";5;"male";"H";64,15606;"smoker"
|
||||||
|
"X40_NORM_";5;"male";"H";58,31063;"nonsmoker"
|
||||||
|
"X88_NORM_";6;"male";"H";24,71469;"nonsmoker"
|
||||||
|
"X125_NORM_";6;"male";"H";37,85341;"smoker"
|
||||||
|
"X139_NORM_";6;"female";"H";46,49144;"smoker"
|
||||||
|
"X60_NORM_";6;"female";"H";55,9506;"nonsmoker"
|
||||||
|
"X105_NORM_";6;"female";"H";20,82957;"nonsmoker"
|
||||||
|
"X114_NORM_";7;"female";"H";22,88569;"nonsmoker"
|
||||||
|
"X135_NORM_";7;"female";"H";20,54768;"smoker"
|
||||||
|
"X77_NORM_";7;"male";"H";59,01711;"nonsmoker"
|
||||||
|
"X158_NORM_";7;"male";"H";52,01916;"smoker"
|
||||||
|
"X42_NORM_";7;"female";"H";23,90691;"nonsmoker"
|
||||||
|
"X147_NORM_";8;"female";"H";22,84189;"smoker"
|
||||||
|
"X98_NORM_";8;"female";"H";42,987;"smoker"
|
||||||
|
"X124_NORM_";8;"male";"H";25,13895;"nonsmoker"
|
||||||
|
"X1_NORM_";8;"male";"H";65,48106;"nonsmoker"
|
||||||
|
"X115_NORM_";8;"female";"H";20,38319;"smoker"
|
||||||
|
"X164_NORM_";9;"female";"H";23,25816;"smoker"
|
||||||
|
"X146_NORM_";9;"female";"H";21,58807;"nonsmoker"
|
||||||
|
"X113_NORM_";9;"male";"H";40,52008;"smoker"
|
||||||
|
"X23_NORM_";9;"male";"H";65,95483;"nonsmoker"
|
||||||
|
"X153_NORM_";10;"female";"H";34,09719;"nonsmoker"
|
||||||
|
"X17_NORM_";10;"female";"H";23,63324;"smoker"
|
||||||
|
"X8_NORM_";10;"male";"H";49,48654;"nonsmoker"
|
||||||
|
"X34_NORM_";10;"male";"H";53,90828;"nonsmoker"
|
||||||
|
"X48_NORM_";10;"female";"H";45,47285;"nonsmoker"
|
||||||
|
"X154_NORM_";11;"female";"H";20,06571;"nonsmoker"
|
||||||
|
"X166_NORM_";11;"male";"H";58,31896;"smoker"
|
||||||
|
"X10_NORM_";11;"male";"H";66,11088;"nonsmoker"
|
||||||
|
"X86_NORM_";11;"male";"H";55,93155;"smoker"
|
||||||
|
"X68_NORM_";11;"female";"H";46,40372;"nonsmoker"
|
||||||
|
"X49_NORM_";11;"male";"H";48,9554;"nonsmoker"
|
||||||
|
"X22_NORM_";11;"male";"H";58,02875;"smoker"
|
||||||
|
"X161_NORM_";12;"male";"H";21,21024;"nonsmoker"
|
||||||
|
"X20_NORM_";12;"male";"H";19,18138;"nonsmoker"
|
||||||
|
"X15_NORM_";12;"male";"H";69,07335;"nonsmoker"
|
||||||
|
"X66_NORM_";12;"male";"H";70,61453;"smoker"
|
||||||
|
"X106_NORM_";12;"male";"H";20,38319;"smoker"
|
||||||
|
"X130_NORM_";13;"female";"H";29,31964;"smoker"
|
||||||
|
"X16_NORM_";13;"male";"H";57,41547;"nonsmoker"
|
||||||
|
"X18_NORM_";13;"female";"H";39,01711;"nonsmoker"
|
||||||
|
"X74_NORM_";13;"male";"H";57,6345;"nonsmoker"
|
||||||
|
"X31_NORM_";14;"female";"H";53,74401;"smoker"
|
||||||
|
"X32_NORM_";14;"male";"H";44,20808;"nonsmoker"
|
||||||
|
"X118_NORM_";14;"male";"H";22,5762;"smoker"
|
||||||
|
"X123_NORM_";14;"female";"H";58,97867;"smoker"
|
||||||
|
"X145_NORM_";14;"male";"H";46,35181;"smoker"
|
||||||
|
"X52_NORM_";14;"male";"H";19,09651;"nonsmoker"
|
||||||
|
"X116_NORM_";15;"male";"H";19,94798;"smoker"
|
||||||
|
"X41_NORM_";15;"female";"H";56,57757;"nonsmoker"
|
||||||
|
"X82_NORM_";15;"male";"H";57,96578;"nonsmoker"
|
||||||
|
"X57_NORM_";15;"female";"H";51,80276;"nonsmoker"
|
||||||
|
"X35_NORM_";16;"male";"H";35,5729;"smoker"
|
||||||
|
"X80_NORM_";16;"female";"H";56,37223;"smoker"
|
||||||
|
"X63_NORM_";16;"female";"H";45,18001;"nonsmoker"
|
||||||
|
"X61_NORM_";16;"female";"H";57,64271;"nonsmoker"
|
||||||
|
"X92_NORM_";17;"female";"H";23,47445;"smoker"
|
||||||
|
"X136_NORM_";17;"male";"H";59,48517;"smoker"
|
||||||
|
"X89_NORM_";17;"female";"H";22,97057;"nonsmoker"
|
||||||
|
"X138_NORM_";17;"female";"H";43,02247;"smoker"
|
||||||
|
"X2_NORM_";17;"male";"H";47,92049;"smoker"
|
||||||
|
"X155_NORM_";17;"female";"H";18,43406;"nonsmoker"
|
||||||
|
"X96_NORM_";18;"female";"H";23,95083;"smoker"
|
||||||
|
"X137_NORM_";18;"male";"H";52,53103;"smoker"
|
||||||
|
"X104_NORM_";18;"male";"H";20,36676;"nonsmoker"
|
||||||
|
"X148_NORM_";18;"female";"H";41,40452;"smoker"
|
||||||
|
"X129_NORM_";19;"male";"H";21,76854;"nonsmoker"
|
||||||
|
"X149_NORM_";19;"male";"H";43,3128;"smoker"
|
||||||
|
"X101_NORM_";19;"male";"H";22,25314;"smoker"
|
||||||
|
"X33_NORM_";19;"female";"H";50,93771;"smoker"
|
||||||
|
"X109_NORM_";19;"male";"H";19,70694;"smoker"
|
||||||
|
"X55_NORM_";20;"male";"H";28,94456;"nonsmoker"
|
|
|
@ -0,0 +1,184 @@
|
||||||
|
X102_NORM_
|
||||||
|
X104_NORM_
|
||||||
|
X105_NORM_
|
||||||
|
X107_210_T05_90026
|
||||||
|
X108_110_T05_90051
|
||||||
|
X108_210_T05_90062
|
||||||
|
X108_NORM_
|
||||||
|
X109_NORM_
|
||||||
|
X10_NORM_
|
||||||
|
X111_110_T02_11651
|
||||||
|
X111_NORM_
|
||||||
|
X112_110_T02_12285
|
||||||
|
X113_NORM_
|
||||||
|
X114_NORM_
|
||||||
|
X122_NORM_
|
||||||
|
X123_NORM_
|
||||||
|
X124_11_T05_90014
|
||||||
|
X124_NORM_
|
||||||
|
X125_NORM_
|
||||||
|
X128_NORM_
|
||||||
|
X129_NORM_
|
||||||
|
X130_NORM_
|
||||||
|
X13_0_T06_90295
|
||||||
|
X1320_0_T03_90210
|
||||||
|
X132_110_T06_90009
|
||||||
|
X1322_0_T04_90118
|
||||||
|
X1323_0_T04_90114
|
||||||
|
X1327_0_T05_90074
|
||||||
|
X133_210_T05_90109
|
||||||
|
X134_110_T04_90117
|
||||||
|
X135_220_T04_90135
|
||||||
|
X135_NORM_
|
||||||
|
X136_NORM_
|
||||||
|
X137_NORM_
|
||||||
|
X138_NORM_
|
||||||
|
X139_NORM_
|
||||||
|
X1401_0_T04_90183
|
||||||
|
X1402_0_T05_90007
|
||||||
|
X1406_0_T04_90217
|
||||||
|
X1408_0_T04_90132
|
||||||
|
X1410_0_T05_90120
|
||||||
|
X1415_0_T07_90003
|
||||||
|
X1417_0_T06_90320
|
||||||
|
X145_NORM_
|
||||||
|
X146_NORM_
|
||||||
|
X147_NORM_
|
||||||
|
X148_NORM_
|
||||||
|
X149_220_T04_90146
|
||||||
|
X149_NORM_
|
||||||
|
X1502_0_T05_90096
|
||||||
|
X1503_0_T06_90169
|
||||||
|
X1505_0_T07_90037
|
||||||
|
X153_NORM_
|
||||||
|
X154_110_T05_90071
|
||||||
|
X154_NORM_
|
||||||
|
X155_NORM_
|
||||||
|
X158_NORM_
|
||||||
|
X159_NORM_
|
||||||
|
X15_NORM_
|
||||||
|
X161_NORM_
|
||||||
|
X163_NORM_
|
||||||
|
X164_NORM_
|
||||||
|
X165_110_T05_90099
|
||||||
|
X166_NORM_
|
||||||
|
X16_NORM_
|
||||||
|
X172_311_T05_90061
|
||||||
|
X175_210_T06_90034
|
||||||
|
X175_311_T05_90103
|
||||||
|
X176_110_T04_90246
|
||||||
|
X17_NORM_
|
||||||
|
X18_110_T05_90100
|
||||||
|
X18_NORM_
|
||||||
|
X195_22_T04_90096
|
||||||
|
X195_311_T06_90020
|
||||||
|
X201_210_T04_90113
|
||||||
|
X201_311_T06_90280
|
||||||
|
X205_110_T04_90200
|
||||||
|
X20_NORM_
|
||||||
|
X216_110_T03_90106
|
||||||
|
X220_110_T04_90021
|
||||||
|
X22_27_T04_90144
|
||||||
|
X22_NORM_
|
||||||
|
X23_220_T05_90086
|
||||||
|
X247_110_T02_07964
|
||||||
|
X24_NORM_
|
||||||
|
X25_0_T06_90258
|
||||||
|
X25_NORM_
|
||||||
|
X28_NORM_
|
||||||
|
X2_NORM_
|
||||||
|
X304_0_T06_90224
|
||||||
|
X3_110_T05_90001
|
||||||
|
X31_NORM_
|
||||||
|
X32_NORM_
|
||||||
|
X33_0_T07_90020
|
||||||
|
X33_110_T02_12543
|
||||||
|
X33_NORM_
|
||||||
|
X353_0_T06_90035
|
||||||
|
X37_110_T06_90046
|
||||||
|
X37_NORM_
|
||||||
|
X391_0_T06_90238
|
||||||
|
X399_0_T06_90196
|
||||||
|
X39_NORM_
|
||||||
|
X40_NORM_
|
||||||
|
X413_0_T06_90159
|
||||||
|
X419_0_T06_90175
|
||||||
|
X41_NORM_
|
||||||
|
X423_0_T06_90237
|
||||||
|
X42_NORM_
|
||||||
|
X43_110_T05_90008
|
||||||
|
X433_0_T06_90135
|
||||||
|
X434_0_T06_90088
|
||||||
|
X450_0_T06_90202
|
||||||
|
X451_0_T06_90027
|
||||||
|
X45_110_T02_10969
|
||||||
|
X454_0_T06_90220
|
||||||
|
X460_0_T06_90266
|
||||||
|
X46_110_T05_90118
|
||||||
|
X464_0_T06_90221
|
||||||
|
X466_0_T06_90045
|
||||||
|
X46_NORM_
|
||||||
|
X474_0_T06_90079
|
||||||
|
X478_0_T06_90151
|
||||||
|
X47_NORM_
|
||||||
|
X487_1_T04_90142
|
||||||
|
X48_NORM_
|
||||||
|
X496_0_T06_90319
|
||||||
|
X4_NORM_
|
||||||
|
X50_110_T02_09087
|
||||||
|
X504_0_T07_90051
|
||||||
|
X51_0_T06_90222
|
||||||
|
X518_0_T06_90188
|
||||||
|
X527_0_T07_90029
|
||||||
|
X530_0_T07_90019
|
||||||
|
X53_22_T04_90131
|
||||||
|
X535_0_T07_90052
|
||||||
|
X543_0_T06_90110
|
||||||
|
X550_0_T07_90049
|
||||||
|
X55_NORM_
|
||||||
|
X57_21_T05_90106
|
||||||
|
X60_210_T06_90065
|
||||||
|
X60_NORM_
|
||||||
|
X613_0_T07_90064
|
||||||
|
X632_0_T07_90050
|
||||||
|
X63_NORM_
|
||||||
|
X641_0_T06_90063
|
||||||
|
X642_0_T07_90030
|
||||||
|
X650_0_T06_90058
|
||||||
|
X658_0_T06_90150
|
||||||
|
X66_0_T06_90281
|
||||||
|
X662_0_T06_90096
|
||||||
|
X66_NORM_
|
||||||
|
X67_0_T06_90307
|
||||||
|
X67_220_T05_90072
|
||||||
|
X68_NORM_
|
||||||
|
X695_0_T06_90053
|
||||||
|
X699_0_T06_90067
|
||||||
|
X71_NORM_
|
||||||
|
X7_21_T04_90179
|
||||||
|
X728_0_T06_90052
|
||||||
|
X730_0_T06_90064
|
||||||
|
X749_0_T06_90080
|
||||||
|
X74_NORM_
|
||||||
|
X76_110_T02_09747
|
||||||
|
X77_110_T05_90091
|
||||||
|
X77_NORM_
|
||||||
|
X78_NORM_
|
||||||
|
X80_11_T04_90157
|
||||||
|
X80_NORM_
|
||||||
|
X81_NORM_
|
||||||
|
X84_NORM_
|
||||||
|
X85_NORM_
|
||||||
|
X86_NORM_
|
||||||
|
X87_110_T06_90007
|
||||||
|
X88_NORM_
|
||||||
|
X89_NORM_
|
||||||
|
X8_NORM_
|
||||||
|
X9_0_T06_90304
|
||||||
|
X96_NORM_
|
||||||
|
X98_110_T02_10430
|
||||||
|
X98_NORM_
|
||||||
|
X99_110_T05_90056
|
||||||
|
X99_220_T05_90057
|
||||||
|
X99_NORM_
|
||||||
|
X263_110_T04_90226_2
|
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue