Search for Variation information by Variation ID:
Detailed information for vg0910354469:
| Variant ID: vg0910354469 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10354469 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
CTTTTTAAAGAAAAGTCCAAGATCTCTTGTGCCATTAAGATATCGAAAGACATTCTTAACTCCAGTCCAATGGCGTTTGGTAGGAGCAGCATTGTATCTT[G/A]
CTAATAGATTTACCGAGAAAGCAATATCTGGCCTCGTACTATTTGCAAGGTACATAAGTGCGCCAATAGCACTAAGATATGGAAAATCAGGTCCAAGCAC
Reverse complement sequence
GTGCTTGGACCTGATTTTCCATATCTTAGTGCTATTGGCGCACTTATGTACCTTGCAAATAGTACGAGGCCAGATATTGCTTTCTCGGTAAATCTATTAG[C/T]
AAGATACAATGCTGCTCCTACCAAACGCCATTGGACTGGAGTTAAGAATGTCTTTCGATATCTTAATGGCACAAGAGATCTTGGACTTTTCTTTAAAAAG
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 | 79.30% | 20.10% | 0.61% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 43.10% | 55.10% | 1.79% | 0.00% | NA |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 64.00% | 34.90% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 16.50% | 80.80% | 2.78% | 0.00% | NA |
| Japonica Intermediate | 241 | 32.40% | 65.60% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 49.00% | 50.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 30.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910354469 | G -> A | LOC_Os09g16930.1 | missense_variant ; p.Ala879Val; MODERATE | nonsynonymous_codon ; A879V | Average:11.909; most accessible tissue: Zhenshan97 flower, score: 19.041 | benign  |
0.876 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910354469 | 5.52E-06 | NA | mr1933_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 |