### Supplementary Data 22:  R code used to identify the sex of the publicly available T. sylvina individual. ###

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# Set parameter and input file here #
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mypath= #Absolute path to Supplementary Table
mySupp="SupplementaryData_21” #Name of Supplementary Table


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# Do the job #
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#Identify sex based on contig classification before adding the publicly available T. sylvina individual
x <- read.table(paste(mypath,"/",mySupp,sep=""),h=T)
xAut <- subset(x, Class_beforeExtra == "autosome")
xSex <- subset(x, Class_beforeExtra == "sexchrom")
w <- wilcox.test(x=xAut$CovExtra,y=xSex$CovExtra,alternative="less",conf.level=level)
pvalw <- round(w$p.value,5)


#Plot raw dataset with cut-off values
pdf(file=paste(mypath,"/SuppFigTsylSex.pdf",sep=""),w=5,h=5)
plot(x$CovExtra ~ x$Class_beforeExtra,col=c("#0000FF40","#FF000040"),xlab="Contig classification before adding the extra individual",ylab="Coverage of the extra individual",ylim=c(0,10),notch=T)
mtext(3,text=paste("Wilcoxon p-value = ",pvalw,sep=""),adj=0,padj=-4.5)
mtext(3,text=paste("median Autosome = ",median(xAut$CovExtra,na.rm=T),sep=""),adj=0,padj=-2.5)
mtext(3,text=paste("median Sex Chrom = ",median(xSex$CovExtra,na.rm=T),sep=""),adj=0,padj=-0.5)
graphics.off()