Search for Variation information by Variation ID:
Detailed information for vg0320861467:
| Variant ID: vg0320861467 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20861467 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.03, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
TACTACGGTAGAGTTGAGCAAATATTGGAGCTAGATTACTTGAAGTTCAAAGTCCCGTTTTTTCGTTGTCGATGGGTCGATCTTCGCAATGTAAAAGTTG[A/C]
CAATGAAGGTTTCACCACTGTCAACTTGGCTAACAACGCATACAAGGATGAACCGTTCGTTCTCGCCAAACAAGTTGTTCAAGTGTTCTACATAGTTGAC
Reverse complement sequence
GTCAACTATGTAGAACACTTGAACAACTTGTTTGGCGAGAACGAACGGTTCATCCTTGTATGCGTTGTTAGCCAAGTTGACAGTGGTGAAACCTTCATTG[T/G]
CAACTTTTACATTGCGAAGATCGACCCATCGACAACGAAAAAACGGGACTTTGAACTTCAAGTAATCTAGCTCCAATATTTGCTCAACTCTACCGTAGTA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.30% | 12.50% | 36.14% | 0.00% | NA |
| All Indica | 2759 | 32.60% | 14.10% | 53.32% | 0.00% | NA |
| All Japonica | 1512 | 87.70% | 11.00% | 1.26% | 0.00% | NA |
| Aus | 269 | 23.40% | 9.30% | 67.29% | 0.00% | NA |
| Indica I | 595 | 17.10% | 11.80% | 71.09% | 0.00% | NA |
| Indica II | 465 | 40.60% | 9.50% | 49.89% | 0.00% | NA |
| Indica III | 913 | 38.60% | 20.70% | 40.74% | 0.00% | NA |
| Indica Intermediate | 786 | 32.70% | 10.80% | 56.49% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 67.10% | 29.80% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.50% | 7.10% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 79.20% | 4.20% | 16.67% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 10.00% | 23.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0320861467 | A -> C | LOC_Os03g37610.1 | missense_variant ; p.Asp765Ala; MODERATE | nonsynonymous_codon ; D765A | Average:27.55; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 | possibly damaging  |
1.623 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320861467 | NA | 1.47E-07 | mr1217 | Jap_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 |
| vg0320861467 | NA | 1.22E-06 | mr1830 | Jap_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 |
| vg0320861467 | NA | 1.88E-08 | mr1136_2 | Jap_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 |
| vg0320861467 | 6.65E-07 | 6.65E-07 | mr1448_2 | Jap_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 |