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can interpreted as とも or ゆう right? So in which word/sentence/context do I use first and when do I pronounce it as another transcription?

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It depends on context: what compound is the character involved in, if any, what are the okurigana and so on.

友達:ともだち (tomodachi)

友人:ゆうじん (yuujin)

There are general rules, like lone kanji, or lone kanji word stems, being kunyomi, and kanji compounds being onyomi. These rules are broken. Sometimes kanji compounds have a kunyomi. Sometimes compounds are half onyomi, half kunyomi.

The ultimate arbiter is the "master" assignment of spellings to the vocabulary.

You just know that yuujin is a word, and tomohito isn't. Ah, but, there is a Tomohito surname, and one way to write it is 友人. You would know that from context, and other clues, like the presence of a given name, or a suffix like さん, 様 (sama), 氏 (shi).

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kunyomi (くにょみ) and onyomi (おにょみ)? Surely you mean kun'yomi (訓読み) and on'yomi (音読み). – Dono Jan 18 '13 at 22:07

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