Search for Variation information by Variation ID:
Detailed information for vg0825508271:
| Variant ID: vg0825508271 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25508271 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 186. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTGAAACCAAAAGCAAATTGTACTTTAAGTCCTCAACCAAAGCTACATTCTTCAATTCAAAATTTTCATTTACCTTAACCAAACCTGTAGCGAGAACG[G/A,T]
CACTTGTAGAAGCATCACCAAAGATAATCGATTCAGTCTTGGATGCCTTCTTAGAGGGAGGAGAACCAATTTTTATCACCGGCCATGTGCCGCGAACAAC
Reverse complement sequence
GTTGTTCGCGGCACATGGCCGGTGATAAAAATTGGTTCTCCTCCCTCTAAGAAGGCATCCAAGACTGAATCGATTATCTTTGGTGATGCTTCTACAAGTG[C/T,A]
CGTTCTCGCTACAGGTTTGGTTAAGGTAAATGAAAATTTTGAATTGAAGAATGTAGCTTTGGTTGAGGACTTAAAGTACAATTTGCTTTTGGTTTCACAA
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 | 63.20% | 18.80% | 11.85% | 5.84% | T: 0.36% |
| All Indica | 2759 | 49.50% | 20.80% | 19.64% | 9.97% | T: 0.04% |
| All Japonica | 1512 | 97.80% | 0.70% | 0.53% | 0.07% | T: 0.93% |
| Aus | 269 | 0.70% | 98.50% | 0.74% | 0.00% | NA |
| Indica I | 595 | 75.30% | 7.60% | 11.60% | 5.55% | NA |
| Indica II | 465 | 72.00% | 9.70% | 12.47% | 5.81% | NA |
| Indica III | 913 | 16.50% | 36.80% | 29.46% | 17.20% | NA |
| Indica Intermediate | 786 | 55.00% | 19.00% | 18.58% | 7.38% | T: 0.13% |
| Temperate Japonica | 767 | 99.20% | 0.50% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 98.00% | 0.80% | 0.60% | 0.00% | T: 0.60% |
| Japonica Intermediate | 241 | 92.90% | 0.80% | 1.66% | 0.00% | T: 4.56% |
| VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 24.40% | 8.89% | 0.00% | T: 2.22% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825508271 | G -> T | LOC_Os08g40290.1 | missense_variant ; p.Ala138Asp; MODERATE | nonsynonymous_codon ; A138D | Average:29.935; most accessible tissue: Zhenshan97 root, score: 43.05 | probably damaging  |
2.089 |
DELETERIOUS | 0.02 |
| vg0825508271 | G -> A | LOC_Os08g40290.1 | missense_variant ; p.Ala138Val; MODERATE | nonsynonymous_codon ; A138V | Average:29.935; most accessible tissue: Zhenshan97 root, score: 43.05 | benign |
0.399 |
TOLERATED | 0.44 |
| vg0825508271 | G -> DEL | LOC_Os08g40290.1 | N | frameshift_variant | Average:29.935; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0825508271 | 2.94E-06 | 2.93E-06 | mr1430 | 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 |
| vg0825508271 | NA | 2.47E-06 | mr1665 | 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 |