Search for Variation information by Variation ID:
Detailed information for vg0220169813:
| Variant ID: vg0220169813 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20169813 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.23, others allele: 0.00, population size: 209. )
Flanking Sequence (100 bp) in Reference Genome:
AACTTCGTTCAGCAGACCCCTTATTTCATCCATGTCTGAATCTTTTGCAGCCTGAAATAGTCTGTTCTGAACCTTGTCGAGCTTTGCAAGCCTTCTGGCA[T/C]
GACTGTTGTCTATCGCAGACCAAATGAAACCAGTCATCCTCCACAAGAGGATTCCGACGTAGATTGCCACGATGCAATCAACACTGTAATGATGGCGCTC
Reverse complement sequence
GAGCGCCATCATTACAGTGTTGATTGCATCGTGGCAATCTACGTCGGAATCCTCTTGTGGAGGATGACTGGTTTCATTTGGTCTGCGATAGACAACAGTC[A/G]
TGCCAGAAGGCTTGCAAAGCTCGACAAGGTTCAGAACAGACTATTTCAGGCTGCAAAAGATTCAGACATGGATGAAATAAGGGGTCTGCTGAACGAAGTT
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 | 58.50% | 41.50% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 64.70% | 34.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 85.00% | 15.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.30% | 98.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.60% | 95.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 35.60% | 63.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220169813 | T -> C | LOC_Os02g33830.1 | missense_variant ; p.His282Arg; MODERATE | nonsynonymous_codon ; H282R | Average:70.357; most accessible tissue: Zhenshan97 root, score: 80.448 | benign  |
-0.427 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220169813 | 3.63E-06 | NA | mr1460_2 | 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 |