Missing readings

Why do some kanji not have onyomi/kunyomi readings, even when my Japanese dictionary lists them?
Why does the program only allow one kind of reading to be used?

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The idea is to learn one thing at a time. You learn the ‘main’ reading when you study the Kanji. Then, later, alternative readings are introduced when learning various Vocabs. If they tried to teach you all the readings at once, it would be overwhelming and hinder learning anything.

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Also, a lot of kanji have readings listed in the dictionary that are almost never used in day-to-day life. When it comes to the Joyo kanji, as well as being a list of the permitted kanji for use in official documents and the like, it’s also a list of the permitted readings.

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A lot of times reading listings in dictionaries are very inclusive, including every possible way a kanji could be read even when those readings are really rare. Consider 保 as in preservation, in basically every jukugo word this will be read as ほ but the dictionaries will list ほう as well. Why? Because there are a handful of rare words where it is read as ほう. Specifically a few era names (保延(ほうえん),保元(ほうげん),保案(ほうあん) etc.) which are spans of about 4ish years each when a specific historic emperor reigned and a really rare word for long life (保命(ほうめい)) which my IDE can’t even type and only shows up in 8 of jpdb’s database of almost 7000 works of fiction.

So you could spend time learning that 保 is sometimes ほう because it’s not impossible for you to encounter it that way. But one of the big goals of WK is to help you to learn kanji in a way that helps you to read quickly. Memorizing all of the readings for a kanji individually without context and then trying to read is a common beginner mistake that WK helps you to avoid.

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Perhaps check JPDB Kanji pages, which list percentages (which is also dependent on the data used to find the Kanji).

Regarding the officially listed readings (in a monolingual), some are rarer than others, while some others might not be that rare, but listed as 表外. It’s also possible that some currently-in-use readings aren’t listed.

About Jisho, Kanji is from Kanjidic, which probably isn’t even official, but volunteered.

WaniKani itself doesn’t use Kanjidic nor monolinguals, but makes the list itself, so sometimes readings are missing. Rarely, WaniKani lists more readings than Jisho.

IMO, eventually what really matter are vocabularies composing of those Kanji, so probably vocabulary frequency. (Still, tbh, some vocabularies are easier to remember than others; so not really just vocab frequency.)