Table 2.

Summary results of the SNPeff analysis of variant effects with respect to transcript structure, reported by category for the putative varietal ‘Nebbiolo’ SNVs. HETERO = heterozygous SNVs; HOMO ALT = homozygous alternate SNVs. Only high-impact SNVs were manually verified and selected for validation.

EFFECT	IMPACT	#HETERO	#HOMO ALT	#TOTAL
START LOST	HIGH MISSENSE	9	37	46
STOP GAINED	HIGH NONSENSE	54	164	218
STOP LOST	HIGH MISSENSE	5	83	88
SPLICE SITE ACCEPTOR	HIGH	15	62	77
SPLICE SITE DONOR	HIGH	15	54	69
NON SYNONYMOUS START	LOW MISSENSE	2	4	6
SYNONYMOUS CODING	LOW SILENT	3,473	11,630	15,103
SYNONYMOUS STOP	LOW SILENT	6	37	43
START GAINED	LOW	136	438	574
NON SYNONYMOUS CODING	MODERATE MISSENSE	3,651	13,125	16,776
DOWNSTREAM	MODIFIER	6,809	35,311	42,120
INTRON	MODIFIER	17,142	99,189	116,331
UPSTREAM	MODIFIER	5,196	27,463	32,659
UTR 3 PRIME	MODIFIER	789	4,639	5,428
UTR 5 PRIME	MODIFIER	799	2,163	2,962