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my %data;
while (<DATA>) {
...
chr2    120  123   X     X    -
chr3    125  130   X     X    -
chr3    131  132   X     X   -

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ID_1    chr1   101   111   3
ID_2    chr1   112   113   1
...
ID_2    chr2   119   123   2
ID_1    chr3   125   130   1
ID_2    chr3   131   132   1