| Variant ID: vg0424199143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24199143 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )
CGTTTCTTTGGTAACCATTGCACAACTTGCAATTGCAGCCATACTAAACTCGCAACATAATACAAAACAATTTAAGACCGGTCAGTCAATGATGTTGATA[G/A]
TTCCAGCTTCGGATGTGTGAAAAAACTGGATGCTTTTGATAGGTGATGTTATTCCCTCATTTATGGCTTTCTTTACCAAATCCCTCTCTATTTTTGTTTG
CAAACAAAAATAGAGAGGGATTTGGTAAAGAAAGCCATAAATGAGGGAATAACATCACCTATCAAAAGCATCCAGTTTTTTCACACATCCGAAGCTGGAA[C/T]
TATCAACATCATTGACTGACCGGTCTTAAATTGTTTTGTATTATGTTGCGAGTTTAGTATGGCTGCAATTGCAAGTTGTGCAATGGTTACCAAAGAAACG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 0.50% | 0.25% | 1.18% | NA |
| All Indica | 2759 | 98.50% | 0.00% | 0.18% | 1.30% | NA |
| All Japonica | 1512 | 98.20% | 1.60% | 0.20% | 0.00% | NA |
| Aus | 269 | 91.80% | 0.00% | 1.12% | 7.06% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.50% | 0.00% | 0.33% | 3.18% | NA |
| Indica Intermediate | 786 | 99.00% | 0.00% | 0.13% | 0.89% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 4.60% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199143 | G -> DEL | LOC_Os04g40780.1 | N | frameshift_variant | Average:46.341; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0424199143 | G -> A | LOC_Os04g40780.1 | missense_variant ; p.Thr429Ile; MODERATE | nonsynonymous_codon ; T429I | Average:46.341; most accessible tissue: Minghui63 root, score: 78.091 | unknown | unknown | DELETERIOUS | 0.00 |