Table 1. Posterior probabilities of inferred ancestral haplotype at the MRCA of SARS-CoV-2.

Positions 8782 and 28144 are indicated in parentheses. Representative genome is that with its sequence matching the haplotype. “No market” excludes 15 market-associated genomes (13 lineage B genomes associated with the Huanan market plus one lineage A and one lineage B genome not associated with the Huanan market). *BF > 10. **BF > 100. ***BF > 1000; BFs are in favor of hypothesis rejection.

Haplotype	Mutations from Hu-1 reference	Representative genome	Phylodynamic analysis
			Unconstrained (%)	No market (%)	recCA (%)
B (C/T)	N/A	Hu-1	80.85†	62.96†	8.18
A (T/C)	C8782T+T28144C	WH04	1.68*	5.73*	77.28†
C/C	T28144C	N/A	10.32	23.02	10.49
T/T	C8782T	N/A	0.92*	1.68*	3.71*
A+C29025T (T/C)	C8782T+T28144C+C29095T	20SF012	<0.01***	<0.01***	0.20**
A.1 (T/C)	C8782T+T28144C+C18060T	WA1	<0.01***	<0.01***	0.04***

†Haplotype with greatest posterior probability; reference for BF.