| Variant ID: vg0433932504 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 33932504 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )
TACATTATCTAAAATAGTAGTTAAAAGCTATGAACGTTAATTTTTTTTAAACTAAGAGCACCTTATATTTTTGGAGGAAGAAAGAACTACCCAGATAAAT[A/T]
ATGACAATGGTGGCAGCTTGCATGCTTGTAAGGCACGGCATTACCTAGCAACAAGCTGATTATAATTTGCGGCTCACCCCTTCTTCTGATAATAGAGGCA
TGCCTCTATTATCAGAAGAAGGGGTGAGCCGCAAATTATAATCAGCTTGTTGCTAGGTAATGCCGTGCCTTACAAGCATGCAAGCTGCCACCATTGTCAT[T/A]
ATTTATCTGGGTAGTTCTTTCTTCCTCCAAAAATATAAGGTGCTCTTAGTTTAAAAAAAATTAACGTTCATAGCTTTTAACTACTATTTTAGATAATGTA
| 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 | 94.70% | 4.20% | 1.12% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 0.40% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 86.00% | 12.40% | 1.59% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica II | 465 | 98.50% | 0.20% | 1.29% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 0.60% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 60.70% | 34.70% | 4.56% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 2.20% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0433932504 | A -> T | LOC_Os04g56910.1 | upstream_gene_variant ; 1821.0bp to feature; MODIFIER | silent_mutation | Average:50.253; most accessible tissue: Callus, score: 86.521 | N | N | N | N |
| vg0433932504 | A -> T | LOC_Os04g56910-LOC_Os04g56920 | intergenic_region ; MODIFIER | silent_mutation | Average:50.253; most accessible tissue: Callus, score: 86.521 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0433932504 | NA | 1.97E-06 | mr1401 | 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 |
| vg0433932504 | 9.35E-06 | 8.43E-10 | mr1277_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 |
| vg0433932504 | NA | 1.76E-09 | mr1746_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 |