R code:

match(df$1GT, df$1XGT)

Will give you the indices for entries 1GT in 1XGT

Now if you want a vector with "concordant"/ "discordant" you can generate a vector of all "discordant" and then use the match command:

tmp<-rep("discordant", nrow(df))
tmp[match(df$1GT, df$1XGT)]<-"concordant"

Something like below, idea is to compare odd columns with even colunns, that is what seq is doing, then use colSums to get sum over TRUE values, then divide by number of rows - number of samples:

#dummy data
df <- data.frame(
  snp1=c(1,1,1,2,2),
  snp1a=c(1,0,1,2,2),
  snp2=c(1,1,1,2,2),
  snp2a=c(1,1,1,2,2),
  snp3=c(1,2,1,2,2),
  snp3a=c(1,2,2,2,2))

df
#   snp1 snp1a snp2 snp2a snp3 snp3a
# 1    1     1    1     1    1     1
# 2    1     0    1     1    2     2
# 3    1     1    1     1    1     2
# 4    2     2    2     2    2     2
# 5    2     2    2     2    2     2

#concordance
colSums(df[,seq(1,ncol(df),2)]==df[,seq(2,ncol(df),2)])/nrow(df)
# snp1 snp2 snp3 
# 0.8  1.0  0.8