| Variant ID: vg0420839533 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20839533 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, G: 0.30, others allele: 0.00, population size: 77. )
CGCCCAGCTCTCCCAATAACAAGGTGAAAGAAATGATCAAAAGAGAAAGGAGAACTTTGCCAACCCAAAGCATCGCTAATAACACACCATTTGCTGCAGA[T/G]
CAACTGGAGATAATATGTTGCGAATCCTCCAGCACTTGCATAGCATGCAATGTTCTGAACCCTCCTAATTTCTTTTTTTTTTCAATTGTACAGCAGACTG
CAGTCTGCTGTACAATTGAAAAAAAAAAGAAATTAGGAGGGTTCAGAACATTGCATGCTATGCAAGTGCTGGAGGATTCGCAACATATTATCTCCAGTTG[A/C]
TCTGCAGCAAATGGTGTGTTATTAGCGATGCTTTGGGTTGGCAAAGTTCTCCTTTCTCTTTTGATCATTTCTTTCACCTTGTTATTGGGAGAGCTGGGCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.90% | 3.60% | 2.60% | 62.82% | NA |
| All Indica | 2759 | 6.90% | 2.10% | 1.09% | 89.96% | NA |
| All Japonica | 1512 | 64.20% | 6.50% | 5.75% | 23.48% | NA |
| Aus | 269 | 77.00% | 2.60% | 0.74% | 19.70% | NA |
| Indica I | 595 | 0.80% | 0.80% | 1.18% | 97.14% | NA |
| Indica II | 465 | 4.90% | 3.00% | 1.29% | 90.75% | NA |
| Indica III | 913 | 8.40% | 1.60% | 0.77% | 89.16% | NA |
| Indica Intermediate | 786 | 10.80% | 2.90% | 1.27% | 84.99% | NA |
| Temperate Japonica | 767 | 82.00% | 2.90% | 3.26% | 11.86% | NA |
| Tropical Japonica | 504 | 35.90% | 12.10% | 10.71% | 41.27% | NA |
| Japonica Intermediate | 241 | 66.80% | 6.60% | 3.32% | 23.24% | NA |
| VI/Aromatic | 96 | 54.20% | 3.10% | 1.04% | 41.67% | NA |
| Intermediate | 90 | 46.70% | 6.70% | 3.33% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420839533 | T -> DEL | N | N | silent_mutation | Average:46.219; most accessible tissue: Callus, score: 76.365 | N | N | N | N |
| vg0420839533 | T -> G | LOC_Os04g34420.1 | upstream_gene_variant ; 3723.0bp to feature; MODIFIER | silent_mutation | Average:46.219; most accessible tissue: Callus, score: 76.365 | N | N | N | N |
| vg0420839533 | T -> G | LOC_Os04g34410.1 | downstream_gene_variant ; 1429.0bp to feature; MODIFIER | silent_mutation | Average:46.219; most accessible tissue: Callus, score: 76.365 | N | N | N | N |
| vg0420839533 | T -> G | LOC_Os04g34410-LOC_Os04g34420 | intergenic_region ; MODIFIER | silent_mutation | Average:46.219; most accessible tissue: Callus, score: 76.365 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420839533 | NA | 3.97E-13 | mr1013 | 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 |
| vg0420839533 | NA | 1.25E-07 | mr1030 | 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 |
| vg0420839533 | NA | 4.55E-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 |
| vg0420839533 | NA | 2.36E-12 | mr1045 | 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 |
| vg0420839533 | NA | 5.85E-06 | mr1046 | 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 |
| vg0420839533 | NA | 2.77E-09 | mr1053 | 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 |
| vg0420839533 | NA | 9.89E-14 | mr1056 | 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 |
| vg0420839533 | NA | 4.11E-06 | mr1058 | 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 |
| vg0420839533 | NA | 5.07E-07 | mr1118 | 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 |
| vg0420839533 | NA | 1.41E-17 | mr1147 | 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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