| Variant ID: vg0820477021 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 20477021 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 82. )
TGTTAATCTATAAGTTTCCGTTCCTATAGTTTGTTAGTTGCTACCATTTTTCTTGGTTTCTTCTATTCCTCAAATTGTCTATTTCCTATAAATTTCAATT[C/T]
TCAGCAGTCACCATGTGACTGCATACCATTTCTATAGTAACATAGCCAACTATTTAATTTCAAATCAGCATCTAGCAACCATTCTTGATACCTAGAATTT
AAATTCTAGGTATCAAGAATGGTTGCTAGATGCTGATTTGAAATTAAATAGTTGGCTATGTTACTATAGAAATGGTATGCAGTCACATGGTGACTGCTGA[G/A]
AATTGAAATTTATAGGAAATAGACAATTTGAGGAATAGAAGAAACCAAGAAAAATGGTAGCAACTAACAAACTATAGGAACGGAAACTTATAGATTAACA
| 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 | 26.50% | 16.20% | 0.97% | 56.31% | NA |
| All Indica | 2759 | 10.00% | 4.10% | 1.59% | 84.31% | NA |
| All Japonica | 1512 | 59.30% | 38.10% | 0.07% | 2.58% | NA |
| Aus | 269 | 0.70% | 1.50% | 0.37% | 97.40% | NA |
| Indica I | 595 | 4.00% | 0.30% | 1.85% | 93.78% | NA |
| Indica II | 465 | 14.20% | 3.70% | 1.72% | 80.43% | NA |
| Indica III | 913 | 10.50% | 5.80% | 1.64% | 82.04% | NA |
| Indica Intermediate | 786 | 11.60% | 5.10% | 1.27% | 82.06% | NA |
| Temperate Japonica | 767 | 75.20% | 24.50% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 37.70% | 56.00% | 0.20% | 6.15% | NA |
| Japonica Intermediate | 241 | 53.50% | 44.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 40.60% | 54.20% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 42.20% | 25.60% | 0.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0820477021 | C -> T | LOC_Os08g33010.1 | downstream_gene_variant ; 3071.0bp to feature; MODIFIER | silent_mutation | Average:26.364; most accessible tissue: Callus, score: 52.648 | N | N | N | N |
| vg0820477021 | C -> T | LOC_Os08g33000.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.364; most accessible tissue: Callus, score: 52.648 | N | N | N | N |
| vg0820477021 | C -> DEL | N | N | silent_mutation | Average:26.364; most accessible tissue: Callus, score: 52.648 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0820477021 | NA | 3.51E-07 | mr1271 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0820477021 | NA | 4.39E-07 | mr1295 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0820477021 | NA | 1.74E-06 | mr1319 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0820477021 | 5.52E-06 | 4.73E-07 | mr1446 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0820477021 | 1.13E-06 | 5.83E-07 | mr1712 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |