| Variant ID: vg0828407010 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 28407010 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 85. )
CAAGTACAGGGAAATATATGGCCCAATTGGCCAACAAACTAGGAAACAACTTATTCCTAAAATCTCTCCTAGCCACTTCCATCTACAGCCGCGGTGATCG[C/T]
GGGCGCGGGCGCAGCTGCGTCGCGCGCGTTTCCCTCGCGTGCTGCTGCGCGCTCCGCCGCTCGGCGGATGTCACGCGCCCTCCTGCGGCGTGTGTATGTC
GACATACACACGCCGCAGGAGGGCGCGTGACATCCGCCGAGCGGCGGAGCGCGCAGCAGCACGCGAGGGAAACGCGCGCGACGCAGCTGCGCCCGCGCCC[G/A]
CGATCACCGCGGCTGTAGATGGAAGTGGCTAGGAGAGATTTTAGGAATAAGTTGTTTCCTAGTTTGTTGGCCAATTGGGCCATATATTTCCCTGTACTTG
| 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 | 42.70% | 17.70% | 3.55% | 36.06% | NA |
| All Indica | 2759 | 15.00% | 22.40% | 2.90% | 59.73% | NA |
| All Japonica | 1512 | 96.00% | 0.90% | 1.46% | 1.65% | NA |
| Aus | 269 | 10.80% | 68.00% | 20.07% | 1.12% | NA |
| Indica I | 595 | 6.60% | 36.50% | 3.87% | 53.11% | NA |
| Indica II | 465 | 15.70% | 12.50% | 2.37% | 69.46% | NA |
| Indica III | 913 | 15.90% | 20.20% | 1.64% | 62.32% | NA |
| Indica Intermediate | 786 | 19.80% | 20.20% | 3.94% | 55.98% | NA |
| Temperate Japonica | 767 | 97.90% | 0.10% | 0.00% | 1.96% | NA |
| Tropical Japonica | 504 | 92.50% | 2.40% | 4.17% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 80.20% | 9.40% | 6.25% | 4.17% | NA |
| Intermediate | 90 | 54.40% | 12.20% | 6.67% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0828407010 | C -> T | LOC_Os08g45240.3 | 3_prime_UTR_variant ; 288.0bp to feature; MODIFIER | silent_mutation | Average:25.615; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828407010 | C -> T | LOC_Os08g45240.2 | intron_variant ; MODIFIER | silent_mutation | Average:25.615; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828407010 | C -> T | LOC_Os08g45240.1 | intron_variant ; MODIFIER | silent_mutation | Average:25.615; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828407010 | C -> T | LOC_Os08g45240.4 | intron_variant ; MODIFIER | silent_mutation | Average:25.615; most accessible tissue: Callus, score: 42.986 | N | N | N | N |
| vg0828407010 | C -> DEL | N | N | silent_mutation | Average:25.615; most accessible tissue: Callus, score: 42.986 | N | N | N | N |