Search for Variation information by Variation ID:
Detailed information for vg0403668263:
| Variant ID: vg0403668263 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3668263 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.14, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TTCTATTATTCCTTTTAGAAAATGATTTTTATTTTGGGATGAATTTATCAGGACGTGACAAAGATGTTCCTTCCCCTTCTCAACAAAACCTTCTGGCTGA[A/G]
AGACATATACTTCTTCCTCAAGATCACCATTAAGGAATGCCGACTTGACGTCAAGGTGATGCACCTGCCACCTTCGATCAGCTGCAACTGCAAGTATAGC
Reverse complement sequence
GCTATACTTGCAGTTGCAGCTGATCGAAGGTGGCAGGTGCATCACCTTGACGTCAAGTCGGCATTCCTTAATGGTGATCTTGAGGAAGAAGTATATGTCT[T/C]
TCAGCCAGAAGGTTTTGTTGAGAAGGGGAAGGAACATCTTTGTCACGTCCTGATAAATTCATCCCAAAATAAAAATCATTTTCTAAAAGGAATAATAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 10.10% | 1.46% | 22.22% | NA |
| All Indica | 2759 | 88.10% | 4.00% | 2.03% | 5.87% | NA |
| All Japonica | 1512 | 19.80% | 23.90% | 0.46% | 55.75% | NA |
| Aus | 269 | 92.20% | 0.00% | 1.49% | 6.32% | NA |
| Indica I | 595 | 97.00% | 1.20% | 0.50% | 1.34% | NA |
| Indica II | 465 | 83.40% | 6.20% | 0.43% | 9.89% | NA |
| Indica III | 913 | 88.40% | 4.70% | 4.05% | 2.85% | NA |
| Indica Intermediate | 786 | 84.00% | 3.80% | 1.78% | 10.43% | NA |
| Temperate Japonica | 767 | 3.10% | 40.30% | 0.65% | 55.93% | NA |
| Tropical Japonica | 504 | 31.00% | 4.40% | 0.40% | 64.29% | NA |
| Japonica Intermediate | 241 | 49.80% | 12.90% | 0.00% | 37.34% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 74.40% | 5.60% | 2.22% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403668263 | A -> DEL | LOC_Os04g06960.1 | N | frameshift_variant | Average:25.219; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg0403668263 | A -> G | LOC_Os04g06960.1 | missense_variant ; p.Phe849Ser; MODERATE | nonsynonymous_codon ; F849S | Average:25.219; most accessible tissue: Minghui63 panicle, score: 38.588 | possibly damaging  |
-1.775 |
TOLERATED | 0.64 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403668263 | 1.96E-06 | NA | mr1588_2 | 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 |