Search for Variation information by Variation ID:
Detailed information for vg0611477699:
| Variant ID: vg0611477699 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11477699 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
GACAAGAACCTGATCCTGGAAGAGGAACAACCTGAGGTGGTGTACCAAGACAAAATTGATCAGACCATGAACTGGCAGAAAACGGAAAGAAACGAGGGAG[T/C]
GTCGTACCTTGGTGGCGGCTCCAATACAGCGCCGATTGCTCAAGAAGATAGCCGCCCACCGTTTGGTTTTGACCTCAATGTTGAGGCTCCAGAACAGGAA
Reverse complement sequence
TTCCTGTTCTGGAGCCTCAACATTGAGGTCAAAACCAAACGGTGGGCGGCTATCTTCTTGAGCAATCGGCGCTGTATTGGAGCCGCCACCAAGGTACGAC[A/G]
CTCCCTCGTTTCTTTCCGTTTTCTGCCAGTTCATGGTCTGATCAATTTTGTCTTGGTACACCACCTCAGGTTGTTCCTCTTCCAGGATCAGGTTCTTGTC
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 | 91.00% | 8.90% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 87.30% | 12.50% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 69.20% | 30.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.10% | 7.40% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 39.60% | 60.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 12.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0611477699 | T -> C | LOC_Os06g20020.1 | missense_variant ; p.Val399Ala; MODERATE | nonsynonymous_codon ; V399A | Average:67.519; most accessible tissue: Callus, score: 91.03 | benign  |
-0.148 |
TOLERATED | 0.89 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0611477699 | 2.99E-06 | 8.34E-09 | mr1697 | 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 |