Search for Variation information by Variation ID:
Detailed information for vg1202830210:
| Variant ID: vg1202830210 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2830210 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 232. )
Flanking Sequence (100 bp) in Reference Genome:
GGAATTTATTTTGCTACTCGTGCTTTCTGTGACAAGCCGAACCACAGGATTGTCCACAAGGATAAAAATCTTGTTAGGGTCGAGAGGGATTTGATTGACG[T/C]
GTTTACACTCCATGAACTTCTGCAGTTATGTGCAAAGAGGAGGTCCCTCTTAGTTGGGAAAAGCTGCCATGGATTAGCCATTCATTTTGGGCTGGTAACT
Reverse complement sequence
AGTTACCAGCCCAAAATGAATGGCTAATCCATGGCAGCTTTTCCCAACTAAGAGGGACCTCCTCTTTGCACATAACTGCAGAAGTTCATGGAGTGTAAAC[A/G]
CGTCAATCAAATCCCTCTCGACCCTAACAAGATTTTTATCCTTGTGGACAATCCTGTGGTTCGGCTTGTCACAGAAAGCACGAGTAGCAAAATAAATTCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.60% | 8.20% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 93.90% | 5.90% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 24.20% | 75.10% | 0.74% | 0.00% | NA |
| Indica I | 595 | 93.10% | 6.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.70% | 6.90% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 4.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202830210 | T -> C | LOC_Os12g06070.1 | missense_variant ; p.Val56Ala; MODERATE | nonsynonymous_codon ; V56A | Average:54.831; most accessible tissue: Callus, score: 79.554 | benign  |
0.134 |
TOLERATED | 0.44 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1202830210 | NA | 6.24E-38 | mr1549 | 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 |
| vg1202830210 | NA | 1.84E-33 | mr1549_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 |
| vg1202830210 | NA | 1.85E-32 | mr1757_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 |
| vg1202830210 | NA | 1.38E-06 | mr1762_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 |