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Reputation is a player statistic. Players have a separate numeric Reputation level/score for each of the three Companies based on the number of items the player or their crew turned in to each Company.
When the reputation hits a certain point you can buy a new tier at the faction the reputation hit that level at.
Higher level tiers have a higher chance of giving better voyages. And at certain levels you can get more maps or chapters. Though this also is no guarantee for the chapter or extra maps to be there. The average loot also increases with higher tiers.