| Variant ID: vg1217385743 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17385743 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 104. )
TTTTACTTCCTATTTTTTCCTTTTACGTTTATTTTCATCTGTAATACCCTACAATATATTTATATCACATGATCTGTTTTTTTTATGTTATTGACTTTTC[A/T]
GCGTATATTTAATTATTTGTCTTAGTATAAAAATTATATAATTATAATAGGAAATCCTACAAATTCCAAAAAAAATAAAACATCCAACCCTCGATTTTCA
TGAAAATCGAGGGTTGGATGTTTTATTTTTTTTGGAATTTGTAGGATTTCCTATTATAATTATATAATTTTTATACTAAGACAAATAATTAAATATACGC[T/A]
GAAAAGTCAATAACATAAAAAAAACAGATCATGTGATATAAATATATTGTAGGGTATTACAGATGAAAATAAACGTAAAAGGAAAAAATAGGAAGTAAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.80% | 6.70% | 3.28% | 37.24% | NA |
| All Indica | 2759 | 53.90% | 11.20% | 5.07% | 29.87% | NA |
| All Japonica | 1512 | 59.20% | 0.10% | 0.26% | 40.48% | NA |
| Aus | 269 | 18.20% | 0.00% | 2.97% | 78.81% | NA |
| Indica I | 595 | 62.50% | 18.50% | 5.71% | 13.28% | NA |
| Indica II | 465 | 56.30% | 8.80% | 3.44% | 31.40% | NA |
| Indica III | 913 | 52.00% | 6.70% | 3.94% | 37.35% | NA |
| Indica Intermediate | 786 | 48.00% | 12.30% | 6.87% | 32.82% | NA |
| Temperate Japonica | 767 | 93.50% | 0.10% | 0.13% | 6.26% | NA |
| Tropical Japonica | 504 | 14.10% | 0.00% | 0.60% | 85.32% | NA |
| Japonica Intermediate | 241 | 44.40% | 0.00% | 0.00% | 55.60% | NA |
| VI/Aromatic | 96 | 18.80% | 1.00% | 1.04% | 79.17% | NA |
| Intermediate | 90 | 52.20% | 5.60% | 2.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217385743 | A -> DEL | N | N | silent_mutation | Average:35.997; most accessible tissue: Callus, score: 80.342 | N | N | N | N |
| vg1217385743 | A -> T | LOC_Os12g29320-LOC_Os12g29330 | intergenic_region ; MODIFIER | silent_mutation | Average:35.997; most accessible tissue: Callus, score: 80.342 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217385743 | NA | 6.78E-06 | mr1302_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 |
| vg1217385743 | NA | 6.65E-06 | mr1813_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 |
| vg1217385743 | NA | 7.31E-06 | mr1824_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 |
| vg1217385743 | 2.83E-06 | NA | mr1889_2 | 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 |