The tone hole position, size, length and shape combined with the bore shape and diameter will depending on the players airspeed and mouthpiece define the sound and intonation of the instrument. We distinguish between
1. Straight tone holes are used primarily on cheap and student instruments. They consist just of a straight cylindrical hole from the outside down to the bore. This will create a stable but inflexible intonation. This is an advantage for beginners, since the tuning of the player will be rather stable and less dependent on their embouchure and airspeed within the piano to mezzo forte dynamic range, usually used by beginners. It helps the beginner also to get used to a correct intonation.
On the other hand, will this reduce the flexibility, appreciated if you like to play with a larger dynamic range or together with other players or t play with bigger musical expression.

2. Tone holes with undercut enlarge their diameter towards the bore. They will allow a bigger dynamic and intonation flexibility. They are therefore the preferred tone hole shape on most professional clarinets.

Ring tone-hole and tone-hole with padseat, both with undercut.

In the past, this tone hole undercutting used to be done by hand, which is one reason why instrument vary in intonation and sound from one to another. The tone-holes on many modern CNC- (computer-numeric-controlled) machined instruments, will have more consistent undercutting.

3. Stepped tone holes are further optimized tone holes primarily seen on oboes. They help to tune the instrument better over several registers.

4. Angled tone holes are very common on bassoons and recorders, but are occasionally also used on clarinets. They help to get the finger position to a more ergonomically location without scarifying the tuning which would require a different tone-hole position.

5. Recommended reading: Good Intonation
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