| Variant ID: vg0409081696 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081696 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 213. )
TTTATTTCTTATGGATGGTTCTTATGCATAAGGATAACTCATCCTAAGAACATCTATTAGGACTACTCCCATAGTATATAATGCCCACTTTAGAGGTCTA[A/G]
GATCCTCCCCTGCGACTACATTAATTGTAGGTGCCCTAAGATTCACATACCAGAGGGGCTTCCCATACTTTTTTTAAGGTAAAACAAAGGCCAGTGTATT
AATACACTGGCCTTTGTTTTACCTTAAAAAAAGTATGGGAAGCCCCTCTGGTATGTGAATCTTAGGGCACCTACAATTAATGTAGTCGCAGGGGAGGATC[T/C]
TAGACCTCTAAAGTGGGCATTATATACTATGGGAGTAGTCCTAATAGATGTTCTTAGGATGAGTTATCCTTATGCATAAGAACCATCCATAAGAAATAAA
| 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 | 65.10% | 34.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 1.10% | 98.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 14.60% | 85.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 51.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081696 | A -> G | LOC_Os04g16680.1 | upstream_gene_variant ; 3808.0bp to feature; MODIFIER | silent_mutation | Average:59.884; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg0409081696 | A -> G | LOC_Os04g16700.1 | downstream_gene_variant ; 3368.0bp to feature; MODIFIER | silent_mutation | Average:59.884; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg0409081696 | A -> G | LOC_Os04g16690.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.884; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |