I mean unique constraint of database, which the field should never have duplicate data. Text file doesn't have such a constraint, sometimes we see duplicate ID in text file. So I think the first thing is to check whether file2 has duplicate ID or not. 

SNP_A-4293670 ss75925050 rs999999
SNP_A-4293670 ss75925050 xxxxxxxx

[download]
This is duplicate ID sample. If file2 has duplicate ID like 'SNP_A-4293670', the result would be overwritten by ' xxxxxxxx'.

In reply to Re^3: Replace data in the column of one file with corresponding ones in another file by remiah
in thread Replace data in the column of one file with corresponding ones in another file by Renyulb28

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