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If I book Manila to São Paulo (with a stopover in Istanbul) on Turkish Airlines I only earn 1,250 miles in my account.
But if I book Manila to Istanbul, it's 7,082 miles. Why does the shorter flight earn more points?
It depends on the fare classes on the tickets. See the following links.
Wikipedia: Fare basis code.
Turkish Airlines: Counting miles based on fare class.
PS: Interesting video explaining fare classes pricing.
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