in reply to compare third column of one file with the first column of another

First you should explain what comprises a "column". In your script, you split both files on /\t/ (a tab), so your ptt.txt (which is one single line, btw.) probably has the word "Location" as first column, and the third column of mapped.txt is the string "gi|448814763|ref|NC_00096".

Most probably that is not what you want.

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