Table 3.

Detection of structural variation in SARS-CoV-2 specimens with ONT sequencing.

Specimen	SV type	Size	Position	Gene	Supporting ONT reads	Short-read evidence	Breakpoint resolution
nCoV_077	Deletion	15	18019-18034	orf1ab	94	Yes	0, 0
nCoV_087	Deletion	1132	1082-2214	orf1ab	48	No	–
nCoV_088	Deletion	34	26786-26820	M	75	Yes	0,0
nCoV_106	Deletion	548	6004-6552	orf1ab	20	No	–
nCoV_125	Deletion	27	27263-27290	ORF6	20	Yes	−2, −3
nCoV_183	Deletion	15	25533-25548	ORF3	41	Yes	−2, −2
nCoV_214	Deletion	29	23554-23583	S	28	Yes	+1, +2
nCoV_200	Deletion	328	27906-28234	ORF8	385	Yes	0, 0
nCoV_209	Deletion	639	2771-3410	orf1ab	48	Yes	0, 0
nCoV_211	Deletion	1840	509-2349	orf1ab	22	No	–
nCoV_225	Deletion	328	27906-28234	ORF8	387	Yes	0, 0
nCoV_235	Deletion	37	26783-26820	M	21	Yes	+3, +4
nCoV_249	Deletion	702	2664-3366	orf1ab	52	Yes	−1, 0
nCoV_164	Deletion	588	22690-23278	S	59	Yes	+1, +4
nCoV_083	Deletion	28	23554-23582	S	38	Yes	0, 0
nCoV_083	Deletion	13	29478-29491	N	36	Yes	+1, +1