console is shrowing False result

Athouse there seems to be no problem in data set . please suggest some some soluction

I think you are confusing rownames of pheno (which look like simple integers to me) with the contents of column x of pheno.

I would agree with @nirgrahamuk on this.

If you are intending for the X column of pheno to be the row names of that table you could try:

Converting the X column of pheno to be rownames using tibble::column_to_rownames()

pheno <- column_to_rownames(pheno, "X")

or importing the first column of your CSV to be row names from the start

pheno <- read.csv("phenotype.csv", row.names = 1)

What may not be guaranteed is that the row names will appear exactly how the column names of count appear, because the original data contains spaces and characters that are not normally allowed in row and column names, so these are converted to a ..