Table 6.
Summary of the predicted effects of SNP and indel variants identified in two Lantana camara differing in female gamete formation.
| Variant Effects | Count | Percentage (%) | Variant Type |
|---|---|---|---|
| Synonymous variant | 51,878 | 33.67 | SNP |
| Missense variant | 45,326 | 29.42 | SNP |
| 3′ UTR variant | 31,145 | 20.22 | SNP |
| 5′ UTR variant | 21,390 | 13.88 | SNP |
| 5′ UTR premature start codon gain variant | 3568 | 2.32 | SNP |
| Stop gained | 529 | 0.34 | SNP |
| Stop lost | 119 | 0.08 | SNP |
| Stop retained variant | 62 | 0.04 | SNP |
| Start lost | 42 | 0.03 | SNP |
| Initiator codon variant | 9 | 0.01 | SNP |
| 3′ UTR variant | 3497 | 39.34 | Indel |
| 5′ UTR variant | 2720 | 30.60 | Indel |
| Frameshift variant | 1029 | 11.58 | Indel |
| Conservative inframe deletion | 516 | 5.80 | Indel |
| Conservative inframe insertion | 471 | 5.30 | Indel |
| Disruptive inframe deletion | 309 | 3.48 | Indel |
| Disruptive inframe insertion | 245 | 2.76 | Indel |
| Stop gained | 49 | 0.55 | Indel |
| Stop lost | 30 | 0.34 | Indel |
| Start lost | 23 | 0.26 | Indel |