| Variant ID: vg0724693113 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 24693113 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 122. )
ATCTACCCAATGGCACGCTTAGAGGTCAATAATAGGACTTTAATTTTGCCGTTTGTTGAGTCGTCTCGTTCGCGTGTAGCTTCGGAGCTCGAAGACCCGG[A/T]
GTGCGCGGATTTCGAGGATCAAGCTCAAGATCTCGAGCAAGGCAAGTCACCTTTGATCATCTTGCACCTATTATTTAAATCTAAATATTTCTTTTCCGCA
TGCGGAAAAGAAATATTTAGATTTAAATAATAGGTGCAAGATGATCAAAGGTGACTTGCCTTGCTCGAGATCTTGAGCTTGATCCTCGAAATCCGCGCAC[T/A]
CCGGGTCTTCGAGCTCCGAAGCTACACGCGAACGAGACGACTCAACAAACGGCAAAATTAAAGTCCTATTATTGACCTCTAAGCGTGCCATTGGGTAGAT
| 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 | 84.30% | 2.80% | 12.23% | 0.66% | NA |
| All Indica | 2759 | 74.70% | 4.30% | 19.90% | 1.12% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 96.70% | 0.00% | 3.35% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 65.20% | 6.00% | 28.17% | 0.65% | NA |
| Indica III | 913 | 62.00% | 5.80% | 29.79% | 2.41% | NA |
| Indica Intermediate | 786 | 76.20% | 4.70% | 18.32% | 0.76% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 10.40% | 9.38% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 3.30% | 10.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724693113 | A -> DEL | N | N | silent_mutation | Average:28.011; most accessible tissue: Zhenshan97 flower, score: 39.624 | N | N | N | N |
| vg0724693113 | A -> T | LOC_Os07g41220-LOC_Os07g41230 | intergenic_region ; MODIFIER | silent_mutation | Average:28.011; most accessible tissue: Zhenshan97 flower, score: 39.624 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0724693113 | 9.49E-06 | NA | mr1120 | 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 |
| vg0724693113 | 7.38E-07 | 2.87E-08 | mr1120 | 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 |
| vg0724693113 | NA | 2.07E-07 | mr1120_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 |
| vg0724693113 | NA | 2.30E-06 | mr1247_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 |