Search for Variation information by Variation ID:
Detailed information for vg0205436718:
| Variant ID: vg0205436718 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 5436718 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
GGGCACCATGCTTTCTTTGTGTTGCTACTTTGTGGGTCTGGGCGCTTGGGAGGGTTCACGTATTCTGCTGCAAGAACTTCCACTTGAGCTTTCCTTTTCC[C/T]
ATTTTTGCGATTTTTCTTTTTGCTTGACTCAGATGCGTCCGTGGCTGGTTTCTTGTCTCCCCCGGTCTTCGGCTTATCGTTCTTGCGTCTTAGCGCATCA
Reverse complement sequence
TGATGCGCTAAGACGCAAGAACGATAAGCCGAAGACCGGGGGAGACAAGAAACCAGCCACGGACGCATCTGAGTCAAGCAAAAAGAAAAATCGCAAAAAT[G/A]
GGAAAAGGAAAGCTCAAGTGGAAGTTCTTGCAGCAGAATACGTGAACCCTCCCAAGCGCCCAGACCCACAAAGTAGCAACACAAAGAAAGCATGGTGCCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.50% | 48.50% | 2.03% | 0.00% | NA |
| All Indica | 2759 | 81.80% | 14.90% | 3.30% | 0.00% | NA |
| All Japonica | 1512 | 1.10% | 98.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 10.40% | 89.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 91.80% | 4.00% | 4.20% | 0.00% | NA |
| Indica II | 465 | 64.90% | 31.80% | 3.23% | 0.00% | NA |
| Indica III | 913 | 85.80% | 11.80% | 2.41% | 0.00% | NA |
| Indica Intermediate | 786 | 79.50% | 16.80% | 3.69% | 0.00% | NA |
| Temperate Japonica | 767 | 1.30% | 98.60% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 85.40% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 28.90% | 70.00% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0205436718 | C -> T | LOC_Os02g10340.1 | missense_variant ; p.Gly496Arg; MODERATE | nonsynonymous_codon ; G496R | Average:26.372; most accessible tissue: Minghui63 flag leaf, score: 39.69 | probably damaging  |
2.607 |
TOLERATED | 0.09 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0205436718 | NA | 9.03E-07 | mr1321 | 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 |