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Name    Chr    Position
rs1    1    35251
...
rs8    21    42516
rs9    4    1110
rs10    4    1145

PGX_SOLEXA1:2:1:5:804#0/1    -    chr1    35245    GGGAGGTAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAA    BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa    0    "24
+:A>N,34:T>N"
PGX_SOLEXA1:2:4:5:804#0/1    +    chr1    37510    TTTTCTTTTTTTTTTTTTT
+TTTTTTTTTTTTTTTTT    BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa    0    "24
+:A>N,34:T>N"
...
PGX_SOLEXA1:15:8:5:314#0/1    -    chr21    42510    GGGGGGTCCCCCCCCCC
+CCCCCCCCCCCCCCCCCCC    BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa    0    "
+24:A>N,34:T>N"
PGX_SOLEXA1:4:9:5:314#0/1    -    chr1    35239    AAAAAAGGGAGGTAAAAAA
+AAAAAAAAAAAAAAAAA    BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa    0    "24
+:A>N,34:T>N"
PGX_SOLEXA1:4:9:21:314#0/1    +    chr4    1110    GAAAAAGGGAGGTAAAAAA
+AAAAAAAAAAAAAAAAG    BB^Yaa^a\a\D\aaaaa`V`a``abbaabaabaaa    0    "24
+:A>N,34:T>N"

!/usr/bin/perl

...
}
close FILE2;
close OUT;