file="chr1 1841 1851 4
chr1 1991 2001 3
chr1 2491 2501 2
chr1 2491 2501 2
chr1 2501 2511 1
chr1 2681 2691 3
chr1 2881 2891 4
chr1 2891 2901 1
chr1 3241 3251 1
chr1 3241 3251 6
"
sort -k 1,3 -k 4r <<< "$file" | awk 'last != $1" "$2" "$3 { print; last = $1" "$2" "$3; }'
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