| Variant ID: vg0209334295 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9334295 |
| 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: 286. )
TCCTAGAACTATTTAATATTATTAATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACC[C/T]
TGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGTTAAGCAGGTTTGAAGAATTAAAACACTAACTTGGGTACATTGCTC
GAGCAATGTACCCAAGTTAGTGTTTTAATTCTTCAAACCTGCTTAACAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCA[G/A]
GGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATTAATAATATTAAATAGTTCTAGGA
| 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 | 51.80% | 0.70% | 2.73% | 44.79% | NA |
| All Indica | 2759 | 28.30% | 0.00% | 3.88% | 67.81% | NA |
| All Japonica | 1512 | 95.20% | 2.00% | 0.26% | 2.51% | NA |
| Aus | 269 | 31.60% | 0.00% | 5.58% | 62.83% | NA |
| Indica I | 595 | 25.40% | 0.00% | 3.87% | 70.76% | NA |
| Indica II | 465 | 33.30% | 0.00% | 3.01% | 63.66% | NA |
| Indica III | 913 | 25.20% | 0.10% | 3.94% | 70.76% | NA |
| Indica Intermediate | 786 | 31.00% | 0.00% | 4.33% | 64.63% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.39% | 1.83% | NA |
| Tropical Japonica | 504 | 94.80% | 1.60% | 0.20% | 3.37% | NA |
| Japonica Intermediate | 241 | 88.00% | 9.10% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209334295 | C -> T | LOC_Os02g16390.1 | upstream_gene_variant ; 1535.0bp to feature; MODIFIER | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0209334295 | C -> T | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg0209334295 | C -> DEL | N | N | silent_mutation | Average:4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |