Table 3.

Mutations lost in sample 9

Position	Mutation	Lineage characteristic of	Sample 1 (%)	Sample 2 (%)	Sample 3 (%)	Sample 4 (%)	Sample 5 (%)	Sample 6 (%)	Sample 7 (%)	Sample 8 (%)	Sample 9 (%)	Annotation	Gene
315	Δ3 bp	Neither	100	100	100	100	100	100	100	100	14.10	coding (50–52/13203 nt)	orf1ab →
1,321	A → C	B.1.1.176	58.60	92.70	86.30	91.70	77.50	23.20	100	100	23.00	E352D (GAA → GAC)	orf1ab →
2,189	C → T	Neither	100	100	100	100	100	100	100	100		L642F (CTT → TTT)	orf1ab →
6,114	C → T	Both	100	100	100	100	100	100	100	100	27.50	P1950L (CCT → CTT)	orf1ab →
6,352	G → T	Neither	100	100	100	100	100	100	100	100	36.10	K2029N (AAG → AAT)	orf1ab →
8,208	C → T	Neither	100	100	100	100	100	100	100	100	37.20	T2648I (ACT → ATT)	orf1ab →
14,767	G → T	B.1.1.176	100	100	100	100	100	100	100	100	30.30	A4835S (GCT → TCT)	orf1ab →
21,621	C → T	B.1.1.176	100	100	100	100	100	100	100	100	37.60	T20I (ACC → ATC) ‡	S →
22,632	G → A	B.1.1.176	100	100	100	100	100	100	100	100	33.30	R357K (AGA → AAA)	S →
25,386	C → T	Neither	100	100	100	100	100	100	100	100	30.70	intergenic (+ 2/-7)	S → / → ORF3a
25,947	G → T	B.1.1.176	100	100	100	100	100	100	100	100	16.60	Q185H (CAG → CAT)	ORF3a →
28,361	G → A	B.1.1.176	100	100	100	100	100	100	100	100	33.40	G30R (GGA → AGA)	N →
28,905	C → T	B.1.1.176	100	100	100	100	100	100	100	100	29.40	A211V (GCT → GTT)	N →

Percentages reflet the proportion of sequencing reads with the listed mutation. "Neither" indicates that the mutation is not characteristic of B.1.1.176 or BA.1. "Both" indicates that the mutation is characteristic of both B.1.1.176 and BA.1, while a blank cell indicates that the listed mutation was present in 0% of reads