| Variant ID: vg0335310070 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310070 |
| Reference Allele: A | Alternative Allele: T,C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.56, A: 0.36, T: 0.07, others allele: 0.00, population size: 45. )
TTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATTCTGACAAATCGACCTTTAATAAAATTTATTTTGAAAATAGACCCAAAATATTCCTT[A/T,C]
CTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACCATTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATATATA
TATATATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACAAATGGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAG[T/A,G]
AAGGAATATTTTGGGTCTATTTTCAAAATAAATTTTATTAAAGGTCGATTTGTCAGAATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAA
| 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 | 58.00% | 24.20% | 0.17% | 0.00% | A: 17.60% |
| All Indica | 2759 | 62.10% | 36.60% | 0.07% | 0.00% | A: 1.20% |
| All Japonica | 1512 | 47.30% | 0.30% | 0.33% | 0.00% | A: 52.05% |
| Aus | 269 | 60.20% | 39.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 76.60% | 21.70% | 0.00% | 0.00% | A: 1.68% |
| Indica II | 465 | 39.10% | 58.30% | 0.22% | 0.00% | A: 2.37% |
| Indica III | 913 | 68.10% | 31.30% | 0.11% | 0.00% | A: 0.44% |
| Indica Intermediate | 786 | 57.80% | 41.20% | 0.00% | 0.00% | A: 1.02% |
| Temperate Japonica | 767 | 11.00% | 0.40% | 0.65% | 0.00% | A: 88.01% |
| Tropical Japonica | 504 | 93.30% | 0.40% | 0.00% | 0.00% | A: 6.35% |
| Japonica Intermediate | 241 | 66.80% | 0.00% | 0.00% | 0.00% | A: 33.20% |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 22.20% | 1.11% | 0.00% | A: 13.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310070 | A -> T | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 239.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0335310070 | A -> T | LOC_Os03g62314.1 | upstream_gene_variant ; 684.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0335310070 | A -> T | LOC_Os03g62340.1 | downstream_gene_variant ; 2381.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0335310070 | A -> C | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 239.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0335310070 | A -> C | LOC_Os03g62314.1 | upstream_gene_variant ; 684.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |
| vg0335310070 | A -> C | LOC_Os03g62340.1 | downstream_gene_variant ; 2381.0bp to feature; MODIFIER | silent_mutation | Average:60.559; most accessible tissue: Minghui63 root, score: 78.091 | N | N | N | N |