Search for Variation information by Variation ID:
Detailed information for vg1125530448:
| Variant ID: vg1125530448 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25530448 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TTTGTGTATAATTTCTGACAGTTGCAAAGATGAATACTTTTATCATAGCTCTGATGCCTATTCTTTGGTATCTGGGCAATGCCATCCAATATTCAGGTCC[G/A]
CTGGGACAGGAAAGCTTCGGATGGTGGAGGATAGACTTATGCAGCAAAAAGCGCAATTGTTACTGGATGAGGCTGCTTCTTGGTCACTTCTTTGGTACCT
Reverse complement sequence
AGGTACCAAAGAAGTGACCAAGAAGCAGCCTCATCCAGTAACAATTGCGCTTTTTGCTGCATAAGTCTATCCTCCACCATCCGAAGCTTTCCTGTCCCAG[C/T]
GGACCTGAATATTGGATGGCATTGCCCAGATACCAAAGAATAGGCATCAGAGCTATGATAAAAGTATTCATCTTTGCAACTGTCAGAAATTATACACAAA
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 | 90.30% | 9.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 73.20% | 26.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 83.40% | 16.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 71.80% | 28.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1125530448 | G -> A | LOC_Os11g42420.1 | missense_variant ; p.Ala177Thr; MODERATE | nonsynonymous_codon ; A177T | Average:46.318; most accessible tissue: Callus, score: 62.534 | benign  |
1.442 |
DELETERIOUS | 0.01 |
| vg1125530448 | G -> A | LOC_Os11g42420.2 | missense_variant ; p.Ala177Thr; MODERATE | nonsynonymous_codon ; A177T | Average:46.318; most accessible tissue: Callus, score: 62.534 | benign |
1.442 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125530448 | 3.56E-06 | NA | mr1238 | 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 |
| vg1125530448 | NA | 7.68E-07 | mr1543 | 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 |
| vg1125530448 | 2.23E-07 | 9.47E-07 | mr1662 | 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 |
| vg1125530448 | 5.22E-06 | 7.21E-07 | mr1662 | 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 |
| vg1125530448 | 3.34E-06 | 7.94E-09 | mr1662_2 | 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 |
| vg1125530448 | 8.41E-06 | 7.07E-06 | mr1662_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 |