>perl -wMstrict -le
"$_ = qq{chr16\t28797601\t-\t0.777877};
 my %site_info;
 ;;
 my @arr = split(/\t/,$_,4);
 $arr[0] = substr($arr[0], 3);
 $site_info{$arr[0]}{$arr[1]}{'strand'} = $arr[2];
 $site_info{$arr[0]{$arr[1]}}{'value'}  = $arr[3];
"
Can't use string ("16") as a HASH ref while "strict refs" in use at ...

##</code><code>##

>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);
 $site_info{$arr[0]}{$arr[1]}{'strand'} = $arr[2];
 $site_info{$arr[0]}{$arr[1]}{'value'}  = $arr[3];
 ;;
 dd \%site_info;
"
{ 16 => { 28797601 => { strand => "-", value => 0.777877 } } }

##</code><code>##

>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 } } }

##</code><code>##

>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);
 ;;
 @{ $site_info{$arr[0]}{$arr[1]} }{ qw(strand value) } = @arr[2, 3];
 ;;
 dd \%site_info;
"
{ 16 => { 28797601 => { strand => "-", value => 0.777877 } } }