Table S1.

Summary of divergences between 496 basic-genome pairs within and between evolutionary groups, limited to perfectly aligned 1-kbp segments from the set of 3,769

			Δ	Δ	Clonal fraction		Δt*
Genome pairs		No.	Min, %	Max, %	Max	Min	Avg, %	SD
A	A	28	0.179	0.876	0.909	0.405	1.393	0.031
B1	B1	28	0.111	0.678	0.956	0.468	1.175	0.016
B2	B2	45	0.034	1.221	0.987	0.147	1.279	0.071
D1	D1	1		1.296		0.200	1.583
D2	D2	1		1.217		0.278	1.658
E	E	1	0.088		0.979
A	B1	64	1.034	1.189	0.271	0.184	1.413	0.016
A	E	16	1.542	1.593	0.071	0.060	1.676	0.013
B1	E	16	1.602	1.629	0.064	0.055	1.706	0.006
D1	D2	4	1.879	2.008	0.049	0.031	2.018	0.044
A	D2	16	2.066	2.119	0.055	0.027	2.168	0.024
B1	D2	16	2.072	2.130	0.031	0.021	2.151	0.022
D2	E	4	2.126	2.162	0.026	0.019	2.189	0.019
B2	D1	20	2.111	2.195	0.040	0.024	2.228	0.017
A	D1	16	2.226	2.265	0.041	0.020	2.317	0.009
B1	D1	16	2.251	2.295	0.028	0.018	2.323	0.010
D1	E	4	2.299	2.314	0.022	0.018	2.350	0.003
B2	D2	20	2.392	2.512	0.017	0.012	2.499	0.030
A	B2	80	2.496	2.566	0.028	0.011	2.578	0.012
B1	B2	80	2.516	2.575	0.016	0.011	2.581	0.012
B2	E	20	2.533	2.578	0.015	0.010	2.594	0.011

^*Excluding genome pairs with clonal fraction >0.9 in A, B1, B2, and E.