Search for Variation information by Variation ID:
Detailed information for vg0321989245:
| Variant ID: vg0321989245 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21989245 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )
Flanking Sequence (100 bp) in Reference Genome:
TAGCACTATATCTTTCTTCAAATTTGATGGGTCTTTCACGTAAAACACTTGTGCCACGCGATTGGCGAGTACCCAAGGGTCATCCTTGTGACCCACACTC[G/A]
CCAGGTCAACAATAGTAAGACCGAACTTATCAACATTGACCCCGTTTGGGTATTTTACCCACTGGCACTTAAATATGGGGAATTGCACTGTGTGCCCATA
Reverse complement sequence
TATGGGCACACAGTGCAATTCCCCATATTTAAGTGCCAGTGGGTAAAATACCCAAACGGGGTCAATGTTGATAAGTTCGGTCTTACTATTGTTGACCTGG[C/T]
GAGTGTGGGTCACAAGGATGACCCTTGGGTACTCGCCAATCGCGTGGCACAAGTGTTTTACGTGAAAGACCCATCAAATTTGAAGAAAGATATAGTGCTA
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 | 46.50% | 36.10% | 1.25% | 16.14% | NA |
| All Indica | 2759 | 11.90% | 58.60% | 2.14% | 27.36% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.07% | NA |
| Aus | 269 | 80.30% | 19.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 10.80% | 20.30% | 3.19% | 65.71% | NA |
| Indica II | 465 | 6.70% | 83.40% | 0.86% | 9.03% | NA |
| Indica III | 913 | 10.40% | 65.40% | 2.52% | 21.69% | NA |
| Indica Intermediate | 786 | 17.70% | 64.90% | 1.65% | 15.78% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 27.80% | 0.00% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321989245 | G -> A | LOC_Os03g39594.1 | missense_variant ; p.Ala264Val; MODERATE | nonsynonymous_codon ; A264V | Average:11.855; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.408 |
DELETERIOUS | 0.03 |
| vg0321989245 | G -> DEL | LOC_Os03g39594.1 | N | frameshift_variant | Average:11.855; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321989245 | NA | 7.85E-06 | mr1030 | 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 |
| vg0321989245 | NA | 2.46E-06 | mr1130 | Ind_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 |
| vg0321989245 | 4.08E-06 | 2.80E-08 | mr1221 | 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 |
| vg0321989245 | NA | 9.42E-09 | mr1637 | 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 |
| vg0321989245 | 1.48E-07 | 1.19E-10 | mr1857 | Ind_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 |