The Latency graph shows the latency in a 50th Percentile, 90th Percentile, or a Histogram View. In the Histogram view, hovering over a box will give you details for that time period. The 50% option shows the median round-trip time for pings used to monitor the site-to-site VPN connection. The 90% option will show you the results of the top 10% of pings.
Typically, use the 50% option to view the average, the 90% option to view spikes in latency over the time period, and the histogram view to get detailed data for a specific time within the time period. When there are network problems (like poor voice quality) that can be related to latency, the 90% or histogram views will help troubleshoot whether those events correlate to VPN latency issues.
https://documentation.meraki.com/MX/Site-to-site_VPN/VPN_Status_Page