| Variant ID: vg0417992105 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17992105 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTGACGCTCTAATAAATTATAGAAATTATGAGAAAAAAATATCAAACTATTGATTTTCATTTAGAATAGTCACCAGTAATTTAAAACATCATATCAAAAT[A/G]
AAATCCCTCTTACCTATATGTACATGCGCCTATCCTCCCCTCATTTTCTCTTTATTTTTTCTTCTTTTTCTAATTAAGGTAGTTATTATGAGATATGCAC
GTGCATATCTCATAATAACTACCTTAATTAGAAAAAGAAGAAAAAATAAAGAGAAAATGAGGGGAGGATAGGCGCATGTACATATAGGTAAGAGGGATTT[T/C]
ATTTTGATATGATGTTTTAAATTACTGGTGACTATTCTAAATGAAAATCAATAGTTTGATATTTTTTTCTCATAATTTCTATAATTTATTAGAGCGTCAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.90% | 2.10% | 2.56% | 37.41% | NA |
| All Indica | 2759 | 56.40% | 0.10% | 2.86% | 40.67% | NA |
| All Japonica | 1512 | 52.10% | 6.40% | 1.39% | 40.08% | NA |
| Aus | 269 | 97.00% | 0.00% | 1.86% | 1.12% | NA |
| Indica I | 595 | 92.80% | 0.00% | 0.17% | 7.06% | NA |
| Indica II | 465 | 33.10% | 0.00% | 3.87% | 63.01% | NA |
| Indica III | 913 | 41.10% | 0.00% | 5.04% | 53.89% | NA |
| Indica Intermediate | 786 | 60.40% | 0.30% | 1.78% | 37.53% | NA |
| Temperate Japonica | 767 | 66.60% | 0.10% | 0.52% | 32.72% | NA |
| Tropical Japonica | 504 | 34.50% | 17.70% | 2.38% | 45.44% | NA |
| Japonica Intermediate | 241 | 42.70% | 2.90% | 2.07% | 52.28% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 12.50% | 8.33% | NA |
| Intermediate | 90 | 61.10% | 2.20% | 4.44% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417992105 | A -> DEL | N | N | silent_mutation | Average:6.371; most accessible tissue: Callus, score: 25.416 | N | N | N | N |
| vg0417992105 | A -> G | LOC_Os04g30150.1 | upstream_gene_variant ; 2232.0bp to feature; MODIFIER | silent_mutation | Average:6.371; most accessible tissue: Callus, score: 25.416 | N | N | N | N |
| vg0417992105 | A -> G | LOC_Os04g30150-LOC_Os04g30160 | intergenic_region ; MODIFIER | silent_mutation | Average:6.371; most accessible tissue: Callus, score: 25.416 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417992105 | 2.11E-07 | 2.15E-06 | mr1925 | 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 |
| vg0417992105 | 6.15E-07 | NA | mr1993_2 | Jap_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 |