| Variant ID: vg0306598450 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6598450 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTTGCTTTCCATGAGGCTGACTAAACTGAACAAGCAATTCGGAGCATGGATTCTGTGCAAGCTAGACCCATCATCAGGTAATCTGTTTGCGGGATCTAG[A/G]
CATGAAATTTGTTTGACATGTGAGGATGTCAGCCTACTTTTGGGAATCCCTTGTGGACGGAAGGAGATTTTGCCTGCAATAAAAAACGAGGTAAAAGATG
CATCTTTTACCTCGTTTTTTATTGCAGGCAAAATCTCCTTCCGTCCACAAGGGATTCCCAAAAGTAGGCTGACATCCTCACATGTCAAACAAATTTCATG[T/C]
CTAGATCCCGCAAACAGATTACCTGATGATGGGTCTAGCTTGCACAGAATCCATGCTCCGAATTGCTTGTTCAGTTTAGTCAGCCTCATGGAAAGCAACC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.70% | 2.50% | 19.00% | 48.79% | NA |
| All Indica | 2759 | 1.40% | 0.00% | 25.88% | 72.67% | NA |
| All Japonica | 1512 | 86.90% | 7.60% | 2.12% | 3.37% | NA |
| Aus | 269 | 0.70% | 0.00% | 24.16% | 75.09% | NA |
| Indica I | 595 | 1.50% | 0.00% | 25.38% | 73.11% | NA |
| Indica II | 465 | 1.90% | 0.00% | 19.57% | 78.49% | NA |
| Indica III | 913 | 0.90% | 0.00% | 33.95% | 65.17% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 20.61% | 77.61% | NA |
| Temperate Japonica | 767 | 96.50% | 0.30% | 0.52% | 2.74% | NA |
| Tropical Japonica | 504 | 69.60% | 20.20% | 4.56% | 5.56% | NA |
| Japonica Intermediate | 241 | 92.50% | 4.60% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 70.83% | 18.75% | NA |
| Intermediate | 90 | 41.10% | 4.40% | 21.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306598450 | A -> DEL | N | N | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598450 | A -> G | LOC_Os03g12470.1 | downstream_gene_variant ; 4413.0bp to feature; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598450 | A -> G | LOC_Os03g12490.1 | downstream_gene_variant ; 3713.0bp to feature; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598450 | A -> G | LOC_Os03g12480.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |