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use strict;
use warnings;
...
1    3.036178    rs32166183    A/C    C    C    C    A
1    3.036265    rs30543887    A/G    G    G    A    A
1    3.039187    rs6365082    G/T    =    =    T    T

snp_id    strain_id    rs_value
1    1    rs31192577
...
3    4    rs30543887
4    3    rs6365082
4    4    rs6365082