| Variant ID: vg0725374751 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25374751 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 350. )
TACAGAAATATCAAAGAATTACCTCAGAGATATCTGTTGAAGCGATGGAGAAGGACTGCCAAGTCTGCAAATGAAGAAAACCAAGGGTATGTGGCAAATG[G/T]
AAATGGTTCATCATTAAATTCCATTGTACCTCCTGCAAACCATCATGGTCTCCAAGGCTTCAGTGCAATGATTCAAGTAACCAATCTGCAAGATTCATTC
GAATGAATCTTGCAGATTGGTTACTTGAATCATTGCACTGAAGCCTTGGAGACCATGATGGTTTGCAGGAGGTACAATGGAATTTAATGATGAACCATTT[C/A]
CATTTGCCACATACCCTTGGTTTTCTTCATTTGCAGACTTGGCAGTCCTTCTCCATCGCTTCAACAGATATCTCTGAGGTAATTCTTTGATATTTCTGTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0725374751 | G -> T | LOC_Os07g42400.2 | missense_variant ; p.Gly691Val; MODERATE | N | Average:53.381; most accessible tissue: Callus, score: 71.998 | N | N | N | N |
| vg0725374751 | G -> T | LOC_Os07g42395.1 | upstream_gene_variant ; 2944.0bp to feature; MODIFIER | N | Average:53.381; most accessible tissue: Callus, score: 71.998 | N | N | N | N |
| vg0725374751 | G -> T | LOC_Os07g42395.2 | upstream_gene_variant ; 2895.0bp to feature; MODIFIER | N | Average:53.381; most accessible tissue: Callus, score: 71.998 | N | N | N | N |
| vg0725374751 | G -> T | LOC_Os07g42400.1 | intron_variant ; MODIFIER | N | Average:53.381; most accessible tissue: Callus, score: 71.998 | N | N | N | N |