| Variant ID: vg0435226140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226140 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 101. )
GCGAGTGATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAG[T/C]
GTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGTGCTCGAGAGGG
CCCTCTCGAGCACCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAAC[A/G]
CTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGATCACTCGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.10% | 14.80% | 10.73% | 27.36% | NA |
| All Indica | 2759 | 11.70% | 25.20% | 17.87% | 45.20% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.13% | 0.53% | NA |
| Aus | 269 | 91.40% | 0.00% | 0.74% | 7.81% | NA |
| Indica I | 595 | 7.20% | 13.60% | 20.34% | 58.82% | NA |
| Indica II | 465 | 6.90% | 20.60% | 22.58% | 49.89% | NA |
| Indica III | 913 | 11.40% | 36.10% | 15.33% | 37.13% | NA |
| Indica Intermediate | 786 | 18.30% | 24.00% | 16.16% | 41.48% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 0.20% | 0.40% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 80.00% | 1.10% | 7.78% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226140 | T -> C | LOC_Os04g59220.1 | synonymous_variant ; p.Ser13Ser; LOW | synonymous_codon | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0435226140 | T -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |