Search for Variation information by Variation ID:
Detailed information for vg0407669199:
| Variant ID: vg0407669199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7669199 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
GAGGTTAAACAATTGTAGCCGATTTGGATGCTTATTAGGAGAAACTTACTGGGATAGCAGGAGCGGCTGGTTGTTCTTCTTCCTCAACATGATGACTTCC[T/C]
ACAGTTGAAGGGGTCTGGTCACTTGACGATTGTTGAGCAGAAGGAGAAGGAGGAGGTGAAGGCTGAAAAGAATGCAAGTGTTAAGTAGAATCGGCTAAAA
Reverse complement sequence
TTTTAGCCGATTCTACTTAACACTTGCATTCTTTTCAGCCTTCACCTCCTCCTTCTCCTTCTGCTCAACAATCGTCAAGTGACCAGACCCCTTCAACTGT[A/G]
GGAAGTCATCATGTTGAGGAAGAAGAACAACCAGCCGCTCCTGCTATCCCAGTAAGTTTCTCCTAATAAGCATCCAAATCGGCTACAATTGTTTAACCTC
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 | 51.80% | 0.30% | 5.40% | 42.47% | NA |
| All Indica | 2759 | 27.60% | 0.50% | 8.23% | 63.68% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.07% | 0.79% | NA |
| Aus | 269 | 22.30% | 0.00% | 1.86% | 75.84% | NA |
| Indica I | 595 | 54.30% | 0.00% | 3.53% | 42.18% | NA |
| Indica II | 465 | 25.40% | 0.60% | 9.03% | 64.95% | NA |
| Indica III | 913 | 8.70% | 0.70% | 11.06% | 79.63% | NA |
| Indica Intermediate | 786 | 30.80% | 0.50% | 8.02% | 60.69% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 68.80% | 1.00% | 19.79% | 10.42% | NA |
| Intermediate | 90 | 67.80% | 2.20% | 3.33% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407669199 | T -> C | LOC_Os04g13750.1 | synonymous_variant ; p.Val694Val; LOW | synonymous_codon | Average:10.929; most accessible tissue: Callus, score: 51.5 | N | N | N | N |
| vg0407669199 | T -> C | LOC_Os04g13750.1 | synonymous_variant ; p.Val694Val; LOW | nonsynonymous_codon ; V694A | Average:10.929; most accessible tissue: Callus, score: 51.5 | benign  |
0.212 |
TOLERATED | 0.81 |
| vg0407669199 | T -> DEL | LOC_Os04g13750.1 | N | frameshift_variant | Average:10.929; most accessible tissue: Callus, score: 51.5 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407669199 | 4.86E-06 | NA | mr1425 | 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 |
| vg0407669199 | NA | 1.52E-07 | mr1425 | Ind_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 |
| vg0407669199 | NA | 3.15E-06 | mr1603 | 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 |
| vg0407669199 | NA | 8.96E-07 | mr1425_2 | Ind_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 |