| Variant ID: vg0233324638 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33324638 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 259. )
TTCCTTTTGAGTTATCATCTGTGTATTTGAATCAAGTGTTCATTACAAACTGATGGGGATTAAAGGAGGAAAAAGGAAAATAATTTCTGCAAAATGTCGA[A/G]
TAATACCCAAAAAAATATATATAGTAGAAACCATTTCATTCCCCAAAATTAACCAACAATGTATAACGCATGTCCAATTCCAATCGATGGATCCTCTGTT
AACAGAGGATCCATCGATTGGAATTGGACATGCGTTATACATTGTTGGTTAATTTTGGGGAATGAAATGGTTTCTACTATATATATTTTTTTGGGTATTA[T/C]
TCGACATTTTGCAGAAATTATTTTCCTTTTTCCTCCTTTAATCCCCATCAGTTTGTAATGAACACTTGATTCAAATACACAGATGATAACTCAAAAGGAA
| 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 | 99.70% | 0.20% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.70% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 4.10% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233324638 | A -> G | LOC_Os02g54370.1 | 3_prime_UTR_variant ; 102.0bp to feature; MODIFIER | silent_mutation | Average:55.26; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |
| vg0233324638 | A -> G | LOC_Os02g54350.1 | upstream_gene_variant ; 4180.0bp to feature; MODIFIER | silent_mutation | Average:55.26; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |
| vg0233324638 | A -> G | LOC_Os02g54360.1 | upstream_gene_variant ; 2099.0bp to feature; MODIFIER | silent_mutation | Average:55.26; most accessible tissue: Zhenshan97 root, score: 68.908 | N | N | N | N |