| Variant ID: vg0234326223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34326223 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
CATGTGCATGATACATCAAACAAAAAATAGTTAATGGTGTGGTTTTATGAAATTATAAAGCCATAATACCTGTGGTTACGTGTAACGCACCAAAACCCCT[A/G]
TGGTTTTGTGCAACTTGGACCATAATACCTAGGGTTTTGTGAAATTTATTCCTTTTTTCCTACTCCGGTGGTTTGCATTCCTTTGCTTCCTTTCGGTATG
CATACCGAAAGGAAGCAAAGGAATGCAAACCACCGGAGTAGGAAAAAAGGAATAAATTTCACAAAACCCTAGGTATTATGGTCCAAGTTGCACAAAACCA[T/C]
AGGGGTTTTGGTGCGTTACACGTAACCACAGGTATTATGGCTTTATAATTTCATAAAACCACACCATTAACTATTTTTTGTTTGATGTATCATGCACATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.20% | 10.60% | 1.21% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 64.40% | 32.00% | 3.64% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 40.90% | 54.50% | 4.56% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 1.20% | 2.78% | 0.00% | NA |
| Japonica Intermediate | 241 | 72.60% | 24.90% | 2.49% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 13.30% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234326223 | A -> G | LOC_Os02g56070.1 | upstream_gene_variant ; 4865.0bp to feature; MODIFIER | silent_mutation | Average:45.016; most accessible tissue: Callus, score: 82.395 | N | N | N | N |
| vg0234326223 | A -> G | LOC_Os02g56080.1 | upstream_gene_variant ; 2137.0bp to feature; MODIFIER | silent_mutation | Average:45.016; most accessible tissue: Callus, score: 82.395 | N | N | N | N |
| vg0234326223 | A -> G | LOC_Os02g56100.1 | upstream_gene_variant ; 2014.0bp to feature; MODIFIER | silent_mutation | Average:45.016; most accessible tissue: Callus, score: 82.395 | N | N | N | N |
| vg0234326223 | A -> G | LOC_Os02g56090.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.016; most accessible tissue: Callus, score: 82.395 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0234326223 | NA | 6.93E-10 | mr1002 | 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 |
| vg0234326223 | NA | 5.13E-09 | mr1002 | Jap_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 |
| vg0234326223 | NA | 1.71E-06 | mr1013 | Jap_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 |
| vg0234326223 | NA | 7.84E-13 | mr1031 | 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 |
| vg0234326223 | NA | 1.62E-06 | mr1031 | Jap_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 |
| vg0234326223 | 5.07E-06 | NA | mr1035 | 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 |
| vg0234326223 | 6.75E-06 | NA | mr1060 | 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 |
| vg0234326223 | NA | 4.86E-07 | mr1077 | Jap_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 |
| vg0234326223 | NA | 3.92E-11 | mr1182 | 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 |
| vg0234326223 | NA | 9.82E-06 | mr1182 | Jap_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 |
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