| Variant ID: vg1208187601 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8187601 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.44, others allele: 0.00, population size: 90. )
CAAGAGAAAGTTGCATAATATTTAACCTCTTGTATTGAGCTAATTATTTTATACATACCGCATATGTGTATCGTTGCATCTTATTTTCCCATAATCCTCC[A/G,T]
TAAGGATTAAACTTTGTTTGTATTGCACATTTGAATAAGTGATTATACATATTGCTCCTATACGTTGATTTATTTCTTATGTTCATAGTAGAACTTATGA
TCATAAGTTCTACTATGAACATAAGAAATAAATCAACGTATAGGAGCAATATGTATAATCACTTATTCAAATGTGCAATACAAACAAAGTTTAATCCTTA[T/C,A]
GGAGGATTATGGGAAAATAAGATGCAACGATACACATATGCGGTATGTATAAAATAATTAGCTCAATACAAGAGGTTAAATATTATGCAACTTTCTCTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 26.70% | 0.40% | 23.89% | T: 0.08% |
| All Indica | 2759 | 50.60% | 37.20% | 0.29% | 11.78% | T: 0.14% |
| All Japonica | 1512 | 51.90% | 4.90% | 0.46% | 42.79% | NA |
| Aus | 269 | 19.30% | 30.50% | 0.74% | 49.44% | NA |
| Indica I | 595 | 38.50% | 45.90% | 0.34% | 15.29% | NA |
| Indica II | 465 | 42.80% | 50.10% | 0.43% | 6.67% | NA |
| Indica III | 913 | 61.00% | 26.90% | 0.11% | 11.50% | T: 0.44% |
| Indica Intermediate | 786 | 52.20% | 35.00% | 0.38% | 12.47% | NA |
| Temperate Japonica | 767 | 75.10% | 6.90% | 0.52% | 17.47% | NA |
| Tropical Japonica | 504 | 23.20% | 2.40% | 0.60% | 73.81% | NA |
| Japonica Intermediate | 241 | 37.80% | 3.70% | 0.00% | 58.51% | NA |
| VI/Aromatic | 96 | 27.10% | 64.60% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 61.10% | 18.90% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208187601 | A -> DEL | N | N | silent_mutation | Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg1208187601 | A -> G | LOC_Os12g14360-LOC_Os12g14374 | intergenic_region ; MODIFIER | silent_mutation | Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg1208187601 | A -> T | LOC_Os12g14360-LOC_Os12g14374 | intergenic_region ; MODIFIER | silent_mutation | Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208187601 | NA | 7.80E-06 | mr1037 | 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 |
| vg1208187601 | NA | 2.99E-07 | mr1049 | 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 |
| vg1208187601 | NA | 8.97E-08 | mr1425 | 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 |
| vg1208187601 | NA | 4.60E-09 | mr1577 | 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 |
| vg1208187601 | NA | 3.72E-07 | mr1864_2 | 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 |