| Variant ID: vg0910529953 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529953 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )
GTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTCACACTGCAGTGGATGTACACTTTACCCGCACTCCG[C/T]
GACTGCCCAACACATGAGCCTCGTCCCAACACATGAGACGCGTCACGGCAAAGCTTTTCGATAACCTCGCATTGGCAGTACCCGCTCCATGAACTTAAAT
ATTTAAGTTCATGGAGCGGGTACTGCCAATGCGAGGTTATCGAAAAGCTTTGCCGTGACGCGTCTCATGTGTTGGGACGAGGCTCATGTGTTGGGCAGTC[G/A]
CGGAGTGCGGGTAAAGTGTACATCCACTGCAGTGTGAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.40% | 0.20% | 11.11% | 78.35% | NA |
| All Indica | 2759 | 3.00% | 0.20% | 14.79% | 82.02% | NA |
| All Japonica | 1512 | 25.10% | 0.00% | 3.90% | 71.03% | NA |
| Aus | 269 | 5.90% | 0.70% | 17.84% | 75.46% | NA |
| Indica I | 595 | 3.70% | 0.30% | 17.48% | 78.49% | NA |
| Indica II | 465 | 1.10% | 0.00% | 11.40% | 87.53% | NA |
| Indica III | 913 | 3.90% | 0.30% | 17.63% | 78.09% | NA |
| Indica Intermediate | 786 | 2.40% | 0.10% | 11.45% | 86.01% | NA |
| Temperate Japonica | 767 | 45.50% | 0.00% | 1.69% | 52.80% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 8.53% | 90.28% | NA |
| Japonica Intermediate | 241 | 10.00% | 0.00% | 1.24% | 88.80% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 4.17% | 93.75% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 6.67% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529953 | C -> DEL | LOC_Os09g17160.1 | N | frameshift_variant | Average:8.931; most accessible tissue: Callus, score: 14.755 | N | N | N | N |
| vg0910529953 | C -> T | LOC_Os09g17160.1 | synonymous_variant ; p.Ser73Ser; LOW | synonymous_codon | Average:8.931; most accessible tissue: Callus, score: 14.755 | N | N | N | N |