Table 3.

Allelic-variant (AV) counts pre/post filtering. AVs= number of all detected AVs; Sites = number of distinct variable sites across SARS-CoV-2 genome; Samples = number of samples in the corresponding dataset. These datasets will also be available from the Viral Beacon project at (https://covid19beacon.crg.eu/).

Dataset	Links	AVs	Sites	Samples
“Boston”	by sample by variant	9,249/8,492	1,027/315	639
“COG-Pre”	by sample by variant	7,338/4,761	2,747/287	503
“COG-Post”	by sample by variant	38,919/38,813	5,760/1,795	1,818