Search for Variation information by Variation ID:
Detailed information for vg1202836219:
| Variant ID: vg1202836219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2836219 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.08, others allele: 0.00, population size: 232. )
Flanking Sequence (100 bp) in Reference Genome:
CCGCCTCCGGCTCCGGGCCGCAGTCGAGGTTAACGCCGAACAGCCTGAGCCGCCTCGACGGCGGCGGCGCCGACGCCGCGCTGCTGCTCTTGGCGTCTGC[T/G]
TCTCTCTGCGACTCTCCTGCAAATTGTTCCACCGCGAAAGGTATATGATCTTTAATCACTTGCTGTAGTTGCATGTTAATTATAGTATCAAAGTGCTTAA
Reverse complement sequence
TTAAGCACTTTGATACTATAATTAACATGCAACTACAGCAAGTGATTAAAGATCATATACCTTTCGCGGTGGAACAATTTGCAGGAGAGTCGCAGAGAGA[A/C]
GCAGACGCCAAGAGCAGCAGCGCGGCGTCGGCGCCGCCGCCGTCGAGGCGGCTCAGGCTGTTCGGCGTTAACCTCGACTGCGGCCCGGAGCCGGAGGCGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.30% | 8.70% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 93.70% | 6.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 20.10% | 79.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.30% | 7.60% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.40% | 7.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202836219 | T -> G | LOC_Os12g06080.1 | missense_variant ; p.Glu212Asp; MODERATE | nonsynonymous_codon ; E212D | Average:75.255; most accessible tissue: Minghui63 panicle, score: 84.005 | benign  |
-0.871 |
TOLERATED | 0.54 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1202836219 | NA | 5.01E-06 | mr1073 | 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 |
| vg1202836219 | NA | 5.54E-06 | mr1545 | 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 |
| vg1202836219 | NA | 2.56E-37 | mr1549 | 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 |
| vg1202836219 | NA | 3.72E-07 | mr1621 | 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 |
| vg1202836219 | NA | 2.08E-36 | mr1757 | 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 |
| vg1202836219 | NA | 3.83E-30 | mr1757_2 | 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 |
| vg1202836219 | NA | 8.22E-07 | mr1762_2 | 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 |