| Variant ID: vg0424199131 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24199131 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 209. )
GTTGACTGAAGCCGTTTCTTTGGTAACCATTGCACAACTTGCAATTGCAGCCATACTAAACTCGCAACATAATACAAAACAATTTAAGACCGGTCAGTCA[A/G]
TGATGTTGATAGTTCCAGCTTCGGATGTGTGAAAAAACTGGATGCTTTTGATAGGTGATGTTATTCCCTCATTTATGGCTTTCTTTACCAAATCCCTCTC
GAGAGGGATTTGGTAAAGAAAGCCATAAATGAGGGAATAACATCACCTATCAAAAGCATCCAGTTTTTTCACACATCCGAAGCTGGAACTATCAACATCA[T/C]
TGACTGACCGGTCTTAAATTGTTTTGTATTATGTTGCGAGTTTAGTATGGCTGCAATTGCAAGTTGTGCAATGGTTACCAAAGAAACGGCTTCAGTCAAC
| 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 | 96.90% | 1.80% | 0.15% | 1.21% | NA |
| All Indica | 2759 | 95.50% | 3.00% | 0.11% | 1.38% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.80% | 0.00% | 1.12% | 7.06% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 89.20% | 7.30% | 0.22% | 3.29% | NA |
| Indica Intermediate | 786 | 97.20% | 1.80% | 0.13% | 0.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199131 | A -> DEL | LOC_Os04g40780.1 | N | frameshift_variant | Average:45.499; most accessible tissue: Minghui63 root, score: 77.29 | N | N | N | N |
| vg0424199131 | A -> G | LOC_Os04g40780.1 | missense_variant ; p.Ile433Thr; MODERATE | nonsynonymous_codon ; I433T | Average:45.499; most accessible tissue: Minghui63 root, score: 77.29 | unknown | unknown | DELETERIOUS | 0.00 |