Search for Variation information by Variation ID:
Detailed information for vg1204313213:
| Variant ID: vg1204313213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4313213 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 42. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGAACAGCGAGAGCGCAAGGATATTGAGGCCACTATCCAAGCTAACCGACAGCTTGTGCATGAAGAGAAATCCAAGCTTGATCAATTATCTGAAGGCC[T/C]
AATCAAGTCTAACATTGATCGGCTTGAGGCTCGCAAAATTGAACTCTTAGCACAACTTGAAGAATGTAACGCTGAACTGGATATAGAGCACAAAAAGCTA
Reverse complement sequence
TAGCTTTTTGTGCTCTATATCCAGTTCAGCGTTACATTCTTCAAGTTGTGCTAAGAGTTCAATTTTGCGAGCCTCAAGCCGATCAATGTTAGACTTGATT[A/G]
GGCCTTCAGATAATTGATCAAGCTTGGATTTCTCTTCATGCACAAGCTGTCGGTTAGCTTGGATAGTGGCCTCAATATCCTTGCGCTCTCGCTGTTCGGC
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 | 24.80% | 3.50% | 17.25% | 54.49% | NA |
| All Indica | 2759 | 6.50% | 3.00% | 22.91% | 67.60% | NA |
| All Japonica | 1512 | 57.90% | 0.60% | 3.04% | 38.49% | NA |
| Aus | 269 | 25.30% | 26.00% | 42.75% | 5.95% | NA |
| Indica I | 595 | 8.60% | 2.90% | 16.13% | 72.44% | NA |
| Indica II | 465 | 8.40% | 2.20% | 18.71% | 70.75% | NA |
| Indica III | 913 | 1.30% | 2.50% | 30.67% | 65.50% | NA |
| Indica Intermediate | 786 | 9.80% | 4.20% | 21.50% | 64.50% | NA |
| Temperate Japonica | 767 | 84.10% | 0.00% | 0.39% | 15.51% | NA |
| Tropical Japonica | 504 | 28.40% | 1.60% | 7.54% | 62.50% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.40% | 2.07% | 61.41% | NA |
| VI/Aromatic | 96 | 15.60% | 2.10% | 5.21% | 77.08% | NA |
| Intermediate | 90 | 36.70% | 2.20% | 18.89% | 42.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204313213 | T -> C | LOC_Os12g08500.1 | missense_variant ; p.Leu429Pro; MODERATE | nonsynonymous_codon ; L429P | Average:9.006; most accessible tissue: Callus, score: 38.455 | benign  |
-0.603 |
TOLERATED | 1.00 |
| vg1204313213 | T -> DEL | LOC_Os12g08500.1 | N | frameshift_variant | Average:9.006; most accessible tissue: Callus, score: 38.455 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204313213 | 5.61E-08 | NA | mr1534 | 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 |