Table 1.

Summary of Solutions Identified by KwARG for Each Sample, and the Probability of Observing the Corresponding Number of Recurrent Mutations.

R	RM	$\mathbb{P}(RM)$	P
(a) South Africa (Nov.)
10	0	0.28	1.00
8	1	0.35	0.72
6	2	0.23	0.37
4	3	0.10	0.14
3	4	0.03	0.04
2	5	0.01	0.01
1	7	0.00	$4\times {10}^{-4}$
0	9	0.00	$7\times {10}^{-6}$
(b) South Africa (Feb.)
7	0	0.52	1.00
5	1	0.34	0.48
3	2	0.11	0.14
2	3	0.03	0.03
1	4	0.00	$5\times {10}^{-3}$
0	5	0.00	$7\times {10}^{-4}$
(c) England (Jan.)
10	0	0.11	1.00
8	1	0.24	0.89
6	2	0.27	0.65
4	3	0.20	0.38
3	4	0.11	0.19
2	5	0.05	0.08
1	6	0.02	0.03
0	14	0.00	$1\times {10}^{-6}$
(d) MERS-CoV
9	0	0.42	1.00
7	1	0.36	0.58
6	2	0.16	0.22
5	3	0.05	0.06
4	4	0.01	0.01
3	5	0.00	$2\times {10}^{-3}$
2	10	0.00	$<1\times {10}^{-6}$
1	12	0.00	$<1\times {10}^{-6}$
0	16	0.00	$<1\times {10}^{-6}$

Note.—First column: number of recombinations. Second column: number of recurrent mutations. Third column: probability of observing a number of recurrent mutations equal to that in the second column. Fourth column: corresponding P values (probability of observing a number of recurrent mutations equal to or greater than that in the second column).