| Variant ID: vg1208153687 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8153687 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 89. )
CTACCTAGCTATGTATATATCTAGTGCCTAGTGGATCAAGACCCATAATTATTTTTCAGTGAAAAGCATGTTGATATATTAGCTCCATTCATCACTTAGT[T/C]
GATCGTGCAATAGTACAGGGTGGGTCATTGCTCTCTCATGATCTCATCCCTGTAATGTTGATCGCCTCTGGTCTCACTGTCTCTCAGCTCTATATATGAA
TTCATATATAGAGCTGAGAGACAGTGAGACCAGAGGCGATCAACATTACAGGGATGAGATCATGAGAGAGCAATGACCCACCCTGTACTATTGCACGATC[A/G]
ACTAAGTGATGAATGGAGCTAATATATCAACATGCTTTTCACTGAAAAATAATTATGGGTCTTGATCCACTAGGCACTAGATATATACATAGCTAGGTAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.00% | 28.30% | 0.51% | 36.16% | NA |
| All Indica | 2759 | 4.60% | 39.90% | 0.58% | 54.98% | NA |
| All Japonica | 1512 | 93.30% | 4.80% | 0.33% | 1.59% | NA |
| Aus | 269 | 16.40% | 30.50% | 0.37% | 52.79% | NA |
| Indica I | 595 | 7.40% | 48.60% | 0.34% | 43.70% | NA |
| Indica II | 465 | 4.70% | 52.90% | 0.22% | 42.15% | NA |
| Indica III | 913 | 2.10% | 29.80% | 0.33% | 67.80% | NA |
| Indica Intermediate | 786 | 5.20% | 37.30% | 1.27% | 56.23% | NA |
| Temperate Japonica | 767 | 92.20% | 6.60% | 0.26% | 0.91% | NA |
| Tropical Japonica | 504 | 94.60% | 2.20% | 0.40% | 2.78% | NA |
| Japonica Intermediate | 241 | 94.20% | 4.10% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 26.00% | 66.70% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 53.30% | 23.30% | 1.11% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208153687 | T -> C | LOC_Os12g14310.1 | upstream_gene_variant ; 403.0bp to feature; MODIFIER | silent_mutation | Average:33.362; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg1208153687 | T -> C | LOC_Os12g14320.1 | downstream_gene_variant ; 1767.0bp to feature; MODIFIER | silent_mutation | Average:33.362; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg1208153687 | T -> C | LOC_Os12g14290-LOC_Os12g14310 | intergenic_region ; MODIFIER | silent_mutation | Average:33.362; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg1208153687 | T -> DEL | N | N | silent_mutation | Average:33.362; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208153687 | 4.58E-06 | 4.58E-06 | mr1424 | Jap_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 |
| vg1208153687 | 3.02E-06 | 1.84E-07 | mr1884 | Jap_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 |
| vg1208153687 | NA | 8.95E-06 | mr1892 | 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 |