Table 1. SARS-CoV-2 proteins with a significantly different rate of mutations as compared to the corresponding background (set of non-structural proteins/set of structural and accessory proteins).

Protein name	Genomic start position	Genomic end position	Length (nt.)	No. of missense mutations	Expected no. of missense mutations	p-value	q-value (FDR corrected)
Proteins under-mutated as compared to the background
nsp4	8555	10054	1500	770	885.71	4.20E-05	8.09E-05
nsp5	10055	10972	918	448	542.05	2.47E-05	5.12E-05
nsp8	12092	12685	594	307	350.74	1.71E-02	2.57E-02
nsp9	12686	13024	339	164	200.17	9.25E-03	1.47E-02
nsp10	13025	13441	417	196	246.23	9.12E-04	1.54E-03
nsp12	13442	16236	2796*	1283	1650.96	9.58E-24	6.46E-23
nsp13	16237	18039	1803	893	1064.62	1.86E-08	5.57E-08
membrane glycoprotein	26523	27191	669	318	523.7	1.44E-23	7.80E-23
surface glycoprotein	21563	25384	3822	2462	2991.87	1.54E-39	4.16E-38
Proteins over-mutated as compared to the background
nsp1	266	805	540	465	318.86	8.02E-15	3.61E-14
nsp2	806	2719	1914	1525	1130.17	7.06E-32	9.53E-31
nsp3	2720	8554	5835	3746	3445.41	2.52E-09	8.50E-09
nsp15	19621	20658	1038	718	612.91	2.16E-05	4.87E-05
Orf3a protein	25393	26220	828	907	648.16	2.99E-24	2.69E-23
Orf6 protein	27202	27387	186	173	145.6	2.36E-02	3.36E-02
Orf7a protein	27394	27759	366	396	286.51	3.70E-10	1.43E-09
Orf8 protein	27894	28259	366	379	286.51	8.65E-08	2.12E-07
nucleocapsid phosphoprotein	28274	29533	1260	1147	986.33	5.41E-08	1.46E-07
Orf14 protein	28734	28955	222	226	173.78	1.18E-04	2.13E-04

*contains a single additional nucleotide because of ribosomal slippage, see Genbank entry for MN908947.3