Search for Variation information by Variation ID:
Detailed information for vg0202301166:
| Variant ID: vg0202301166 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2301166 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
AGGTATATACCGATCACAAGAGTTTAAAGTATATCTTTACTCAGCCGGATCTGAACATGAGACAACGGAGATGGTTGGAACTAATTAAGGATTATGACAT[A/G]
GGAATTCATTATCACCCGGGAAAGGCTAATGTTGTAGCAGACGCTCTTAGTAGAAAAGGCTATTGCAATGCTACGGAAGGACGACAGCTGCCATTGGAAT
Reverse complement sequence
ATTCCAATGGCAGCTGTCGTCCTTCCGTAGCATTGCAATAGCCTTTTCTACTAAGAGCGTCTGCTACAACATTAGCCTTTCCCGGGTGATAATGAATTCC[T/C]
ATGTCATAATCCTTAATTAGTTCCAACCATCTCCGTTGTCTCATGTTCAGATCCGGCTGAGTAAAGATATACTTTAAACTCTTGTGATCGGTATATACCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.20% | 38.90% | 12.06% | 4.85% | NA |
| All Indica | 2759 | 55.60% | 32.30% | 8.77% | 3.30% | NA |
| All Japonica | 1512 | 17.00% | 57.30% | 16.80% | 8.93% | NA |
| Aus | 269 | 72.50% | 11.50% | 15.99% | 0.00% | NA |
| Indica I | 595 | 54.60% | 26.90% | 11.76% | 6.72% | NA |
| Indica II | 465 | 73.80% | 18.70% | 4.30% | 3.23% | NA |
| Indica III | 913 | 43.20% | 45.30% | 9.53% | 1.97% | NA |
| Indica Intermediate | 786 | 60.10% | 29.40% | 8.27% | 2.29% | NA |
| Temperate Japonica | 767 | 0.50% | 89.60% | 3.26% | 6.65% | NA |
| Tropical Japonica | 504 | 44.80% | 15.10% | 32.94% | 7.14% | NA |
| Japonica Intermediate | 241 | 11.20% | 42.70% | 26.14% | 19.92% | NA |
| VI/Aromatic | 96 | 74.00% | 7.30% | 18.75% | 0.00% | NA |
| Intermediate | 90 | 33.30% | 48.90% | 14.44% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202301166 | A -> G | LOC_Os02g04940.1 | missense_variant ; p.Ile1143Met; MODERATE | nonsynonymous_codon ; I1143M | Average:16.079; most accessible tissue: Zhenshan97 flower, score: 25.98 | benign  |
-0.124 |
TOLERATED | 1.00 |
| vg0202301166 | A -> DEL | LOC_Os02g04940.1 | N | frameshift_variant | Average:16.079; most accessible tissue: Zhenshan97 flower, score: 25.98 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202301166 | 3.94E-06 | 6.55E-10 | mr1798_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 |