I have downloaded a gene transcript file from GENCODE genes and when I examine the transcript support level column, I notice that missing values are recorded as both "NA" and NA.

library(rtracklayer)
G25 <- import.gff3("gencode.v25.annotation.gff3")
> head(mcols(G25)[, "transcript_support_level"])
[1]  NA  "1" "1" "1" "1" "NA"

The missing values are in some cases inadvertently recorded as a character string.