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.
From: Whole-genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones
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 |
