Table 2.

Structural domain-wise distribution of the major mutation-types detected across spike protein-encoding genes in 71,703 complete SARS-CoV-2 whole-genomes sequenced globally until 21 August 2020.

Domains of SARS-CoV-2 spike protein (span in amino acid positions)	No. of mutations detected	No. of missense mutations	No. of synonymous mutations	No. of stops generated due to mutations	No. of C➔U transitions (NCU)	NCU resulting in non-synomymous mutations	No. of G➔U transversions (NGU)	NGU resulting in missense mutations
Upstream region	3a	0	0	0	1	0	0	0
Signal peptide (1−13)	38	24	14	0	6	4	4	4
N-terminal Domain or NTD (14–305)	696	468	221	7	101	58	85	77
Peptide linking NTD with Receptor Binding Domain or RBD (306–318)	31	21	10	0	5	2	1	1
RBD (319–541)	375	208	157	10	61	24	33	29
Peptide linking RBD with Fusion Peptide or FP (542–787)	464	295	165	4	98	63	46	41
FP (788–806)	37	26	11	0	4	3	2	2
Peptide linking FP with Heptapeptide Repeat Sequence or HR1 (807–911)	227	140	85	2	41	23	28	25
HR1 (912–984)	130	78	51	1	24	11	17	17
Peptide linking HR1 with Heptapeptide Repeat Sequence or HR2 (985–1162)	315	192	118	5	51	32	46	41
HR2 (1163–1213)	101	72	29	0	14	6	14	14
Transmembrane domain (1213–1237)	50	32	18	0	5	1	15	14
Cytoplasmic domain (1237–1273)	87	59	27	1	17	7	18	17
Splice region	2b	0	0	0	0	0	0	0
Total	2556	1615	906	30	428	234	309	282

^aThese three mutations have non-coding effect.

^bOne of these two mutations involved stop loss and the other a stop retention.