Search for Variation information by Variation ID:
Detailed information for vg0716335289:
| Variant ID: vg0716335289 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16335289 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
AGTTGAACCAGTTCACGTAAAGCTGGTCATCACTAAGCTGTGTTATTTCTTCAATTGCATATCTCAGAAAGTAATTGATCTTGAAGAGTTAGGTCCTCTC[T/C]
GGGCTTTCGCTATACAGACAGTGTGCGAGCTTGAGATGTGTTTCCCTCCATCATTTTTCGATATGATGCAACACCTCATAGTTCATATCATGCCTCAAAT
Reverse complement sequence
ATTTGAGGCATGATATGAACTATGAGGTGTTGCATCATATCGAAAAATGATGGAGGGAAACACATCTCAAGCTCGCACACTGTCTGTATAGCGAAAGCCC[A/G]
GAGAGGACCTAACTCTTCAAGATCAATTACTTTCTGAGATATGCAATTGAAGAAATAACACAGCTTAGTGATGACCAGCTTTACGTGAACTGGTTCAACT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.60% | 36.20% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 96.20% | 3.50% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.90% | 6.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.80% | 1.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.60% | 1.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 91.70% | 7.80% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 4.60% | 95.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 48.90% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0716335289 | T -> C | LOC_Os07g28000.1 | missense_variant ; p.Trp544Arg; MODERATE | nonsynonymous_codon ; W544R | Average:17.075; most accessible tissue: Callus, score: 46.941 | probably damaging  |
-3.161 |
TOLERATED | 0.65 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716335289 | NA | 2.04E-28 | mr1075 | 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 |
| vg0716335289 | NA | 1.79E-36 | mr1719 | 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 |
| vg0716335289 | NA | 1.52E-07 | mr1170_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 |
| vg0716335289 | 4.77E-06 | NA | mr1183_2 | Ind_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 |
| vg0716335289 | NA | 2.07E-06 | mr1754_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 |