| Variant ID: vg0207059780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 7059780 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.05, others allele: 0.00, population size: 100. )
ACTCATCCACCCTAAAGACGGAACCGTGGTAGTCTTGGATCCTCTCAATTACAGTCACAGGCAATACAAAGAATTTCTAACAATCTTACAGTAGTAAGTG[A/T]
TTATAACTCTTGCATTTCTATATGAATGTATTATAAATAAATATCCTCCTTAATATGAAACGGTACGACATCCATACAGTGCATACCAATACTACAAGTT
AACTTGTAGTATTGGTATGCACTGTATGGATGTCGTACCGTTTCATATTAAGGAGGATATTTATTTATAATACATTCATATAGAAATGCAAGAGTTATAA[T/A]
CACTTACTACTGTAAGATTGTTAGAAATTCTTTGTATTGCCTGTGACTGTAATTGAGAGGATCCAAGACTACCACGGTTCCGTCTTTAGGGTGGATGAGT
| 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 | 50.10% | 44.30% | 0.87% | 4.74% | NA |
| All Indica | 2759 | 27.10% | 69.90% | 0.69% | 2.32% | NA |
| All Japonica | 1512 | 97.10% | 2.40% | 0.07% | 0.46% | NA |
| Aus | 269 | 21.90% | 32.00% | 5.58% | 40.52% | NA |
| Indica I | 595 | 28.90% | 70.80% | 0.17% | 0.17% | NA |
| Indica II | 465 | 20.40% | 74.00% | 0.65% | 4.95% | NA |
| Indica III | 913 | 27.80% | 70.10% | 0.55% | 1.53% | NA |
| Indica Intermediate | 786 | 28.90% | 66.50% | 1.27% | 3.31% | NA |
| Temperate Japonica | 767 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 2.80% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.50% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 50.00% | 4.20% | 5.21% | 40.62% | NA |
| Intermediate | 90 | 51.10% | 42.20% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0207059780 | A -> T | LOC_Os02g13250.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:55.011; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0207059780 | A -> T | LOC_Os02g13260.1 | upstream_gene_variant ; 3057.0bp to feature; MODIFIER | silent_mutation | Average:55.011; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0207059780 | A -> T | LOC_Os02g13240.1 | downstream_gene_variant ; 4391.0bp to feature; MODIFIER | silent_mutation | Average:55.011; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0207059780 | A -> DEL | N | N | silent_mutation | Average:55.011; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0207059780 | NA | 1.11E-06 | mr1338 | 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 |
| vg0207059780 | 2.66E-06 | 2.66E-06 | mr1828 | 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 |
| vg0207059780 | NA | 2.37E-06 | mr1881 | 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 |