initial <-read.table....
library(Mass)

glm.percent <- glm.nb(cbind(Count, Rest)~ Plasmid+Region*Plasmid, data=initial)

   Error in x[good, , drop = FALSE] : (subscript) logical subscript too long

'data.frame':   54 obs. of  4 variables:
              $ Plasmid: Factor w/ 2 levels "CTR","EXP": 2 2 2 2 2 2 2 2 2 2 ...
              $ Region : Factor w/ 6 levels "L0","L1","L2+3",..: 2 2 2 2 2 3 3 3 3 3 ...
              $ Count  : int  0 3 34 12 83 361 426 185 402 565 ...
              $ Rest   : int  464 592 306 482 791 103 169 155 92 309 ...