Search for Variation information by Variation ID:
Detailed information for vg0336059373:
| Variant ID: vg0336059373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 36059373 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
TCTGGGCGCTTGGGAGGGTTCGCGTATTCTGCTGCGAGGACTTCCGCTTGAGCTTTCCTTTTCCCATTTTTGCGATTCTTCTTCTTGCTTGACTCAGGTG[C/T]
GTCAGTGGCTGATTTCTTCTCTCCCCCGGTCTTCGGCTTATCGTTCTTGCGTCTTAGCGCATCATCTGCGTGGGCGCATCGCTCAACAATCTCGAACAAT
Reverse complement sequence
ATTGTTCGAGATTGTTGAGCGATGCGCCCACGCAGATGATGCGCTAAGACGCAAGAACGATAAGCCGAAGACCGGGGGAGAGAAGAAATCAGCCACTGAC[G/A]
CACCTGAGTCAAGCAAGAAGAAGAATCGCAAAAATGGGAAAAGGAAAGCTCAAGCGGAAGTCCTCGCAGCAGAATACGCGAACCCTCCCAAGCGCCCAGA
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 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 91.40% | 8.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.20% | 14.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0336059373 | C -> T | LOC_Os03g63830.1 | missense_variant ; p.Ala515Thr; MODERATE | nonsynonymous_codon ; A515T | Average:30.065; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | benign  |
0.097 |
TOLERATED | 0.19 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0336059373 | NA | 3.05E-07 | mr1553 | 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 |
| vg0336059373 | 5.08E-06 | NA | mr1726 | 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 |
| vg0336059373 | 1.17E-06 | 7.09E-07 | mr1892 | 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 |