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perl -pane 'print "$F[0]\t$F[1]\t$F[2]";' file1.txt

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prints:
chr1    58963   Gchr1    58963   G       G       10      0       10   
+   1       ^+.     8

__file1__
chr1    58963   G       G       10      0       10      1       ^+.   
+  8