Table 5.

Allelic-variants (AVs) with maximum allele frequency < 80% overlapping with codons under selection. % samp = fraction of samples containing a given AV in each dataset

POS	R	A	Gene	AA	% samp	mean	min	max	codon
“Boston”
25,842	A	C	orf3a	T151P	6.259	0.083	0.051	0.180	ACT
22,254	A	G	S	I231M	2.034	0.066	0.050	0.102	ATA
“COG-Pre”
21,637	C	T	S	P26S	0.397	0.520	0.260	0.779	CCT
22,343	G	T	S	G261V	0.397	0.425	0.091	0.758	GGT
28,825	C	T	N	R185C	0.397	0.619	0.528	0.709	CGT
“COG-Post”
1,463	G	A	nsp2	G220D	0.715	0.737	0.669	0.767	GGT
22,343	G	T	S	G261V	0.660	0.703	0.672	0.737	GGT
25,217	G	T	S	G1219V	0.330	0.752	0.746	0.756	GGT
21,845	C	T	S	T95I	0.275	0.466	0.069	0.731	ACT
29,252	C	T	N	S327L	0.220	0.196	0.083	0.359	TCG
29,170	C	T	N	H300Y	0.165	0.314	0.076	0.735	CAT
4,441	G	T	nsp3	V575L	0.110	0.725	0.712	0.739	GTG
21,829	G	T	S	V90F	0.110	0.508	0.242	0.774	GTT
28,394	G	A	N	R41Q	0.110	0.318	0.054	0.582	CGG
29,446	G	T	N	V392L	0.110	0.770	0.765	0.774	GTG