DELLY junction types?

TRA have all four types of junction (3to3, 3to5, 5to3, 5to5)

These are the CT INFO lines. “Paired-end signature induced connection type”

I draw the long part of each chr as a thick line and telomeres as a circle. I assume each event needs to end up with two telomeres, and that all TRA events join the entire length of the two chomosomes. This may be incorrect??

5’ DEL are always 3to5 (all DELs are CT=3to5)

A

3’

3’

5’

3’

chr1 Reference D starts like 3’ chr2 this

B C

5’ E

5’

3’ 5’ 3’ 5’ F G

H

One possibilty:

3to5 5’ DUP are always 5to3 (all DUPs areCT=5to3)

A

3’ 5’

3’

3’ 5’

5to3

3’

A

B

3’

5’

C

D

3to3 at one end

3’ 5’ D

5’

3’ 5’ B

3’ D

and the reciprocal

Another possibilty:

INVs have two types of junction

A

3’ 5’ 5to3

5’

5’

H

F C

E

this

B G

5to3 5’

5’

3’

3’ 5’

C

E

A

3’ F

5’

3’

E

F

5to5 at the other

3’ Reference starts like this Inversion is like this

H

3’ 3’ B F

3to3

5’ and the reciprocal

E

5’ 5’

3’

GC

5to5

NB: We also get CT=3to5 TRA junctions, but I don’t know where these come from.

D

DELLY junction types? -

DUP are always 5to3 (all DUPs areCT=5to3). 3'. 5'. INVs have two ... “Paired-end signature induced connection type”. A. B C. D E. F. A. B D. C E. F. A. B C. D. E.

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