Table 2.

Variants noted in specimens A and B compared with the reference genome

		Coverage (reads)	Allele frequency (%)	Forward/reverse balance*	Average quality†
Shared variants of specimens A and B versus reference genome
241C→T
	Specimen A	67	100%	0·37	35·6
	Specimen B	6	100%	0·38	36·0
1059C→T
	Specimen A	144	100%	0·48	35·6
	Specimen B	55	92·7%	0·26	35·4
3037C→T
	Specimen A	89	100%	0·42	35·6
	Specimen B	425	99·8%	0·19	35·5
14408C→T‡
	Specimen A	73	100%	0·40	35·7
	Specimen B	1145	99·6%	0·43	35·6
23403A→G
	Specimen A	6859	99·9%	0·19	35·7
	Specimen B	10 484	99·9%	0·46	35·6
25563G→T
	Specimen A	421	100%	0·45	35·2
	Specimen B	757	99·1%	0·48	35·4
Specimen A-specific variants versus reference genome
539C→T		141	99·3%	0·45	35·6
4113C→T		159	70·4%	0·38	35·6
7921A→G		182	98·9%	0·49	35·7
16741G→T		173	99·4%	0·47	35·6
Specimen B-specific variants versus reference genome
8140C→T		1046	85·0%	0·43	35·6
11102C→T		1713	99·9%	0·44	35·5
14407C→T‡		1145	99·7%	0·43	35·6
15190G→C		139	90·6%	0·33	35·7
15981C→T		224	100%	0·38	35·5
26013C→T		1415	99·2%	0·38	35·5
29466C→T		86	98·8%	0·07	35·8

Reference genome was Wuhan Hu 1 (GenBank MN908947.3).

^*Ratio of forward to reverse reads covering the locus.

^†Phred score. Phred is a measure of base calling accuracy, a higher score indicates higher quality. A Phred score of 30 indicates a base-calling accuracy of 99·9%.

^‡CLC Genomics classified this variant as a dinucleotide multinucleotide variant. The two variants have been split in this table for clarity.