Search for Variation information by Variation ID:
Detailed information for vg0601059247:
| Variant ID: vg0601059247 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1059247 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, A: 0.40, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
TAAATTTGACCTTTTAGAACTATTTAAGGACTTTCATTCTGGGAGTTTGCCTTTATATTCGCTTAACTTTGGTACTATCATTCTTTTGCCTAAGTGTGCT[A/G]
AGGCTTTAAAGATTCAACAATATAGACCTATATGCCTACTTAATGTTAGCTTTAAGATTTTTACCAAAGTTGCTACAAATAGAATAATGGATGTTGCCCA
Reverse complement sequence
TGGGCAACATCCATTATTCTATTTGTAGCAACTTTGGTAAAAATCTTAAAGCTAACATTAAGTAGGCATATAGGTCTATATTGTTGAATCTTTAAAGCCT[T/C]
AGCACACTTAGGCAAAAGAATGATAGTACCAAAGTTAAGCGAATATAAAGGCAAACTCCCAGAATGAAAGTCCTTAAATAGTTCTAAAAGGTCAAATTTA
Allele Frequencies:
| 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 | 55.10% | 11.20% | 30.36% | 3.36% | NA |
| All Indica | 2759 | 41.90% | 12.00% | 44.22% | 1.88% | NA |
| All Japonica | 1512 | 90.70% | 0.30% | 2.78% | 6.22% | NA |
| Aus | 269 | 3.70% | 39.80% | 55.76% | 0.74% | NA |
| Indica I | 595 | 70.40% | 5.00% | 22.52% | 2.02% | NA |
| Indica II | 465 | 62.40% | 5.20% | 29.46% | 3.01% | NA |
| Indica III | 913 | 14.20% | 20.20% | 64.29% | 1.31% | NA |
| Indica Intermediate | 786 | 40.50% | 11.70% | 46.06% | 1.78% | NA |
| Temperate Japonica | 767 | 93.60% | 0.00% | 3.00% | 3.39% | NA |
| Tropical Japonica | 504 | 84.10% | 0.20% | 2.78% | 12.90% | NA |
| Japonica Intermediate | 241 | 95.00% | 1.70% | 2.07% | 1.24% | NA |
| VI/Aromatic | 96 | 6.20% | 82.30% | 3.12% | 8.33% | NA |
| Intermediate | 90 | 64.40% | 10.00% | 22.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601059247 | A -> G | LOC_Os06g02880.1 | missense_variant ; p.Lys540Glu; MODERATE | nonsynonymous_codon ; K540E | Average:24.016; most accessible tissue: Minghui63 young leaf, score: 33.985 | benign  |
-0.65 |
TOLERATED | 1.00 |
| vg0601059247 | A -> DEL | LOC_Os06g02880.1 | N | frameshift_variant | Average:24.016; most accessible tissue: Minghui63 young leaf, score: 33.985 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601059247 | 5.74E-06 | 5.74E-06 | mr1300 | Ind_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 |
| vg0601059247 | 2.65E-06 | 2.42E-06 | mr1310 | Ind_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 |