| Variant ID: vg0315630241 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15630241 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )
AGATCTTGGAAGAAAAAATGACGAAAGAACCTAAAATAGCCCTGAAAATTTTAGCACCTAATTTAAGACTTTCTAGGTCTGTTTTGGGCCTTGGGCCAAC[T/A]
TGTTGTATTCAACTCTCTTCTCTAATGGAATGCCATGCAAAGCTTTTGCGTGCTCCCCACAAAAGAATTTTTTATAACAACATCGATACAGTAAAAGGCA
TGCCTTTTACTGTATCGATGTTGTTATAAAAAATTCTTTTGTGGGGAGCACGCAAAAGCTTTGCATGGCATTCCATTAGAGAAGAGAGTTGAATACAACA[A/T]
GTTGGCCCAAGGCCCAAAACAGACCTAGAAAGTCTTAAATTAGGTGCTAAAATTTTCAGGGCTATTTTAGGTTCTTTCGTCATTTTTTCTTCCAAGATCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 1.60% | 0.76% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.20% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 94.40% | 4.60% | 0.99% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.00% | 1.85% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.00% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 84.70% | 12.90% | 2.38% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 1.70% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315630241 | T -> A | LOC_Os03g27270.1 | downstream_gene_variant ; 3037.0bp to feature; MODIFIER | silent_mutation | Average:58.023; most accessible tissue: Callus, score: 85.639 | N | N | N | N |
| vg0315630241 | T -> A | LOC_Os03g27280.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.023; most accessible tissue: Callus, score: 85.639 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315630241 | NA | 3.11E-06 | mr1027_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 |
| vg0315630241 | NA | 9.50E-07 | mr1217_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 |
| vg0315630241 | 2.85E-06 | 2.85E-06 | mr1333_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 |