| Variant ID: vg1201984316 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1984316 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 318. )
AGAGGAAGCGTTCAGTGTATTCTATTTTGACGGTGATGGGTTCATATGTTCCTTAGAGTTGCAAAATGTGATGATAAGGATGCTAGGTATGAGGACTGTG[A/G]
AAAGATGATTCATGTTTTTGACAAAGATGGTGATGGCAGGATTAGATTGGATGAGTTCAGAGCTGTGTGACTAAAACCTCTTTCTTGTTAAGTTTAACTG
CAGTTAAACTTAACAAGAAAGAGGTTTTAGTCACACAGCTCTGAACTCATCCAATCTAATCCTGCCATCACCATCTTTGTCAAAAACATGAATCATCTTT[T/C]
CACAGTCCTCATACCTAGCATCCTTATCATCACATTTTGCAACTCTAAGGAACATATGAACCCATCACCGTCAAAATAGAATACACTGAACGCTTCCTCT
| 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 | 56.40% | 0.10% | 13.08% | 30.39% | NA |
| All Indica | 2759 | 32.00% | 0.30% | 21.42% | 46.36% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.13% | 0.07% | NA |
| Aus | 269 | 36.80% | 0.00% | 7.43% | 55.76% | NA |
| Indica I | 595 | 35.80% | 0.70% | 23.53% | 40.00% | NA |
| Indica II | 465 | 33.80% | 0.00% | 18.06% | 48.17% | NA |
| Indica III | 913 | 23.00% | 0.10% | 21.25% | 55.64% | NA |
| Indica Intermediate | 786 | 38.40% | 0.30% | 22.01% | 39.31% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 4.44% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201984316 | A -> DEL | LOC_Os12g04680.1 | N | frameshift_variant | Average:62.813; most accessible tissue: Zhenshan97 root, score: 76.397 | N | N | N | N |
| vg1201984316 | A -> G | LOC_Os12g04680.1 | missense_variant ; p.Glu58Gly; MODERATE | nonsynonymous_codon ; E58G | Average:62.813; most accessible tissue: Zhenshan97 root, score: 76.397 | unknown | unknown | DELETERIOUS | 0.00 |