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How does Tor determine what country a node is based in? For ex, tracerouting this current relay ip 45.32.55.55 shows it is from Japan, but Tor tags it as being from the Netherlands

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IP geolocation is generally not an exact science, and similar anomalies have been discussed before: Why does hard coded node 'Faravahar' have a different geolocation (USA) than registrar (Mauritius)?

For example, this site (and others like it) check several different databases, and give several different results for the IP address you're looking at (including both Japan and the Netherlands, but also France).

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