>perl -wMstrict -le
"use Data::Dump qw(dd);
 ;;
 $_ = qq{chr16\t28797601\t-\t0.777877};
 my %site_info;
 ;;
 my @arr = split(/\t/,$_,4);
 $arr[0] = substr($arr[0], 3);
 ;;
 my $current = $site_info{$arr[0]}{$arr[1]} = {};
 $current->{'strand'} = $arr[2];
 $current->{'value'}  = $arr[3];
 ;;
 dd \%site_info;
"
{ 16 => { 28797601 => { strand => "-", value => 0.777877 } } }