beta_mp_f[,1][beta_mp_f[,1] == 1648] <- 4
beta_mp_f[,1][beta_mp_f[,1] == 1647] <- 18
beta_mp_f[,1][beta_mp_f[,1] == 1646] <- 3
beta_mp_f[,1][beta_mp_f[,1] == 1645] <- 8
beta_mp_f[,1][beta_mp_f[,1] == 1644] <- 14
beta_mp_f[,1][beta_mp_f[,1] == 1642] <- 7
beta_mp_f[,1][beta_mp_f[,1] == 1641] <- 9
beta_mp_f[,1][beta_mp_f[,1] == 1640] <- 15
beta_mp_f[,1][beta_mp_f[,1] == 1639] <- 10
beta_mp_f[,1][beta_mp_f[,1] == 1638] <- 19
beta_mp_f[,1][beta_mp_f[,1] == 1636] <- 5
beta_mp_f[,1][beta_mp_f[,1] == 1632] <- 13
beta_mp_f[,1][beta_mp_f[,1] == 1633] <- 21
beta_mp_f[,1][beta_mp_f[,1] == 1631] <- "Z"
beta_mp_f[,1][beta_mp_f[,1] == 1628] <- 1
beta_mp_f[,1][beta_mp_f[,1] == 1627] <- 22
beta_mp_f[,1][beta_mp_f[,1] == 1095] <- 21
beta_mp_f[,1][beta_mp_f[,1] == 833] <- 12
beta_mp_f[,1][beta_mp_f[,1] == 588] <- 20
beta_mp_f[,1][beta_mp_f[,1] == 833] <- 12
beta_mp_f[,1][beta_mp_f[,1] == 503] <- 16
beta_mp_f[,1][beta_mp_f[,1] == 309] <- 17
beta_mp_f[,1][beta_mp_f[,1] == 228] <- 6
beta_mp_f[,1][beta_mp_f[,1] == 11] <- 2
beta_mp_f[,1][beta_mp_f[,1] == 4] <- 11
beta_mp_f[,1][beta_mp_f[,1] == 270] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 1643] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 1650] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 1635] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 1558] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 1136] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 385] <- "NA"
beta_mp_f[,1][beta_mp_f[,1] == 255] <- "NA"
The extra scaffolds in the data have the following depth which I used to drop 4 scaffolds since plink uses only 95 chromosomes.