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 chrM    2928    A    G    17    0    0%    A    46    105    69.54%  
+  R    Somatic    1    1.23052720566294E-008    17    29    50    55 
+   4    13    0    0 
 chr1    108310    T    C    9    0    0%    T    3    5    62.5%    Y
+    Somatic    1    0.0090497738    2    1    2    3    7    2    0  
+  0 
 chr1    726958    T    A    11    0    0%    T    9    4    30.77%   
+ W    Somatic    1    0.0672877847    6    3    1    3    5    6    0
+    0 
 chr1    1412720    C    A    33    0    0%    C    22    6    21.43% 
+   M    Somatic    1    0.0067850063    10    12    3    3    14    1
+9    0    0 
chr1    1822396    C    G    6    0    0%    C    4    4    50%    S  
+  Somatic    1    0.0699300699    3    1    2    2    4    2    0    
+0 
 chr1    1822457    C    T    10    0    0%    C    4    4    50%    Y
+    Somatic    1    0.022875817    3    1    2    2    6    4    0   
+ 0

 while (my $line = <FILE>) {
    next if ($. == 1);
    chomp $line;
...
    

}