Search for Variation information by Variation ID:
Detailed information for vg0321873587:
| Variant ID: vg0321873587 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21873587 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTCGGCATGCAGGGTACTTTTGGCCGACAATGCTAGAGGATTGTTTCAGATATTATAAGGGGTGTCAGGATTGTCAGAAGTTTGGAGCAATTCAGCGAG[C/T]
GCCGGCGTCAGCTATGAATCCTATTATTAAGCCATGGCCGTTCAGAGGTTGGGGAATTGATATAATCAGTATGATAAACCCACCATCGAGTAAAGGGCAT
Reverse complement sequence
ATGCCCTTTACTCGATGGTGGGTTTATCATACTGATTATATCAATTCCCCAACCTCTGAACGGCCATGGCTTAATAATAGGATTCATAGCTGACGCCGGC[G/A]
CTCGCTGAATTGCTCCAAACTTCTGACAATCCTGACACCCCTTATAATATCTGAAACAATCCTCTAGCATTGTCGGCCAAAAGTACCCTGCATGCCGAAG
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 | 69.40% | 2.20% | 3.34% | 25.03% | NA |
| All Indica | 2759 | 51.10% | 3.70% | 5.47% | 39.72% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.13% | 1.46% | NA |
| Aus | 269 | 81.80% | 0.00% | 0.37% | 17.84% | NA |
| Indica I | 595 | 82.70% | 4.50% | 2.86% | 9.92% | NA |
| Indica II | 465 | 40.00% | 4.50% | 6.02% | 49.46% | NA |
| Indica III | 913 | 38.70% | 0.30% | 6.79% | 54.22% | NA |
| Indica Intermediate | 786 | 48.10% | 6.60% | 5.60% | 39.69% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.40% | 4.17% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 4.44% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321873587 | C -> T | LOC_Os03g39350.1 | missense_variant ; p.Ala1310Val; MODERATE | nonsynonymous_codon ; A1310V | Average:34.828; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 | benign  |
0.9 |
DELETERIOUS | 0.04 |
| vg0321873587 | C -> DEL | LOC_Os03g39350.1 | N | frameshift_variant | Average:34.828; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321873587 | 3.07E-06 | 9.58E-07 | mr1689 | 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 |