| Variant ID: vg0202004329 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2004329 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 250. )
AGATATTTACCGGAAATTTCATTTGTTTTTTGCAGACTGGTCAAGAAACAGACATTGTTTTGGTTTCATGCACAGGCTCTGGAATCGAACCTAACAGAAG[A/G]
GAACAAGTCCTCAAAGCAAAGAAGGTATCACTTCTCATAACCACACATCAAATGCAAACTGTTCTTGATGCACTCTTGATACAAACATTAACCAGTTTAT
ATAAACTGGTTAATGTTTGTATCAAGAGTGCATCAAGAACAGTTTGCATTTGATGTGTGGTTATGAGAAGTGATACCTTCTTTGCTTTGAGGACTTGTTC[T/C]
CTTCTGTTAGGTTCGATTCCAGAGCCTGTGCATGAAACCAAAACAATGTCTGTTTCTTGACCAGTCTGCAAAAAACAAATGAAATTTCCGGTAAATATCT
| 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 | 96.80% | 3.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.90% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 87.70% | 12.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 2.70% | 0.00% | 0.00% | 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% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202004329 | A -> G | LOC_Os02g04510.1 | synonymous_variant ; p.Arg484Arg; LOW | synonymous_codon | Average:54.936; most accessible tissue: Minghui63 flag leaf, score: 84.227 | N | N | N | N |