| Variant ID: vg0420889762 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20889762 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGAGAGGGTTGCCGGTGGAGGTGGAGGATGAAGAGGAAGCCATGACAATCTATGCCAATAGGCTCTGATACCATGAAAGAAAACTAATATGGAGTAACG[T/C]
TATCGGTGCGGAGAAAATTGACATTTAGCCACTTTCAAGGATGGGTTTCGCTGTAATGCCATTCCGCCAACTTGCTTCGCTAAAATGCCATTCCCACGCT
AGCGTGGGAATGGCATTTTAGCGAAGCAAGTTGGCGGAATGGCATTACAGCGAAACCCATCCTTGAAAGTGGCTAAATGTCAATTTTCTCCGCACCGATA[A/G]
CGTTACTCCATATTAGTTTTCTTTCATGGTATCAGAGCCTATTGGCATAGATTGTCATGGCTTCCTCTTCATCCTCCACCTCCACCGGCAACCCTCTCTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.70% | 9.10% | 1.18% | 46.93% | NA |
| All Indica | 2759 | 17.10% | 1.50% | 1.88% | 79.49% | NA |
| All Japonica | 1512 | 79.60% | 20.20% | 0.00% | 0.26% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 2.70% | 2.70% | 2.86% | 91.76% | NA |
| Indica II | 465 | 13.10% | 0.90% | 1.72% | 84.30% | NA |
| Indica III | 913 | 24.90% | 0.70% | 1.64% | 72.84% | NA |
| Indica Intermediate | 786 | 21.50% | 1.90% | 1.53% | 75.06% | NA |
| Temperate Japonica | 767 | 97.90% | 1.70% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 65.70% | 34.10% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 50.20% | 49.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 25.00% | 71.90% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 61.10% | 18.90% | 4.44% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420889762 | T -> C | LOC_Os04g34490.1 | upstream_gene_variant ; 4142.0bp to feature; MODIFIER | silent_mutation | Average:22.869; most accessible tissue: Callus, score: 48.35 | N | N | N | N |
| vg0420889762 | T -> C | LOC_Os04g34510.1 | upstream_gene_variant ; 2482.0bp to feature; MODIFIER | silent_mutation | Average:22.869; most accessible tissue: Callus, score: 48.35 | N | N | N | N |
| vg0420889762 | T -> C | LOC_Os04g34520.1 | downstream_gene_variant ; 3578.0bp to feature; MODIFIER | silent_mutation | Average:22.869; most accessible tissue: Callus, score: 48.35 | N | N | N | N |
| vg0420889762 | T -> C | LOC_Os04g34500.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.869; most accessible tissue: Callus, score: 48.35 | N | N | N | N |
| vg0420889762 | T -> DEL | N | N | silent_mutation | Average:22.869; most accessible tissue: Callus, score: 48.35 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420889762 | 4.40E-06 | 2.39E-09 | mr1554 | 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 |
| vg0420889762 | NA | 1.95E-06 | mr1695 | 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 |
| vg0420889762 | NA | 2.86E-07 | mr1183_2 | 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 |
| vg0420889762 | NA | 7.06E-07 | mr1554_2 | 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 |