| Variant ID: vg0206047310 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6047310 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 331. )
ATACTATTAAATACATGTATGAAACTGATGGTCCTTGTCCAGCAGGATTTGCAGCCGGGATCTTCGGTACTGGGGCCTCTTCGTCTCACGCCGGTAGGAC[T/G]
GGTCCTACTAGCCAGTTCTACGACGACGACTTGCACGGTGCACACCACCACGACGTACTAGGCTCCTCTCAGCTTGGAGGAGCTCCAGAGGCGCACACTC
GAGTGTGCGCCTCTGGAGCTCCTCCAAGCTGAGAGGAGCCTAGTACGTCGTGGTGGTGTGCACCGTGCAAGTCGTCGTCGTAGAACTGGCTAGTAGGACC[A/C]
GTCCTACCGGCGTGAGACGAAGAGGCCCCAGTACCGAAGATCCCGGCTGCAAATCCTGCTGGACAAGGACCATCAGTTTCATACATGTATTTAATAGTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.30% | 0.70% | 2.41% | 63.58% | NA |
| All Indica | 2759 | 0.80% | 0.20% | 2.10% | 96.88% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.00% | 2.38% | NA |
| Aus | 269 | 0.40% | 9.30% | 18.96% | 71.38% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.50% | 99.16% | NA |
| Indica II | 465 | 0.90% | 0.00% | 2.37% | 96.77% | NA |
| Indica III | 913 | 0.80% | 0.00% | 2.63% | 96.60% | NA |
| Indica Intermediate | 786 | 1.10% | 0.80% | 2.54% | 95.55% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.00% | 1.96% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 4.17% | 58.33% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 1.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206047310 | T -> G | LOC_Os02g11730.1 | synonymous_variant ; p.Thr1497Thr; LOW | synonymous_codon | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0206047310 | T -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |