1-base overlaps:

Augmenting GFF3 data...
Sorting...
Finding intersects...
Total unique peaks: 9500
Overlaps with five_prime_utr      :    1754 (18%)
Overlaps with three_prime_utr     :     165 ( 1%)
Overlaps with intron              :    3995 (42%)
Overlaps with exon                :     161 ( 1%)
Overlaps with upstream1000        :     166 ( 1%)
Overlaps with upstream10000       :     654 ( 6%)
Overlaps with upstream100000      :    1904 (20%)
Overlaps with upstream-beyond     :     312 ( 3%)

20% peak overlaps:

Using existing ../Mus_musculus.GRCm38.100-augmented.bed...
Using existing ../Mus_musculus.GRCm38.100-augmented+sorted.bed...
Finding intersects...
Total unique peaks: 9500
Overlaps with five_prime_utr      :    1091 (11%)
Overlaps with three_prime_utr     :     137 ( 1%)
Overlaps with intron              :    4410 (46%)
Overlaps with exon                :     314 ( 3%)
Overlaps with upstream1000        :     271 ( 2%)
Overlaps with upstream10000       :     666 ( 7%)
Overlaps with upstream100000      :    1909 (20%)
Overlaps with upstream-beyond     :     362 ( 3%)

20% GFF feature overlaps:

Using existing ../Mus_musculus.GRCm38.100-augmented.bed...
Using existing ../Mus_musculus.GRCm38.100-augmented+sorted.bed...
Finding intersects...
Total unique peaks: 9500
Overlaps with five_prime_utr      :    1711 (18%)
Overlaps with three_prime_utr     :     107 ( 1%)
Overlaps with intron              :     418 ( 4%)
Overlaps with exon                :     437 ( 4%)
Overlaps with upstream1000        :     229 ( 2%)
Overlaps with upstream10000       :       0 ( 0%)
Overlaps with upstream100000      :       0 ( 0%)
Overlaps with upstream-beyond     :    3109 (32%)

20% either peak or GFF feature overlaps:

Using existing ../Mus_musculus.GRCm38.100-augmented.bed...
Using existing ../Mus_musculus.GRCm38.100-augmented+sorted.bed...
Finding intersects...
Total unique peaks: 9500
Overlaps with five_prime_utr      :    1754 (18%)
Overlaps with three_prime_utr     :     165 ( 1%)
Overlaps with intron              :    3995 (42%)
Overlaps with exon                :     161 ( 1%)
Overlaps with upstream1000        :     166 ( 1%)
Overlaps with upstream10000       :     654 ( 6%)
Overlaps with upstream100000      :    1904 (20%)
Overlaps with upstream-beyond     :     312 ( 3%)

Midpoints only:

Using existing ../Mus_musculus.GRCm38.100-augmented.bed...
Using existing ../Mus_musculus.GRCm38.100-augmented+sorted.bed...
Finding intersects...
Total unique peaks: 9500
Overlaps with five_prime_utr      :     667 ( 7%)
Overlaps with three_prime_utr     :     113 ( 1%)
Overlaps with intron              :    4344 (45%)
Overlaps with exon                :     380 ( 4%)
Overlaps with upstream1000        :     684 ( 7%)
Overlaps with upstream10000       :     679 ( 7%)
Overlaps with upstream100000      :    1929 (20%)
Overlaps with upstream-beyond     :     422 ( 4%)
