Search for Variation information by Variation ID:
Detailed information for vg1209592277:
| Variant ID: vg1209592277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9592277 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.01, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
CATATTGATCTTTGGAAATAGCCTCAATGTGATTGAGGAGGTTAAGGACTTTCTGTCCAAGGGTTTTGAAATGAAGGATTTGGGAGAGGCTAATGTTATC[C/A]
TTAACATTAAGCTACTAAGAGGAGCTGAGGGTGGGATTACACTTGTGCAATCCCACTATGTGGACATGGTTTTGAGTCGCTTTGGATATAGTGACTGCAA
Reverse complement sequence
TTGCAGTCACTATATCCAAAGCGACTCAAAACCATGTCCACATAGTGGGATTGCACAAGTGTAATCCCACCCTCAGCTCCTCTTAGTAGCTTAATGTTAA[G/T]
GATAACATTAGCCTCTCCCAAATCCTTCATTTCAAAACCCTTGGACAGAAAGTCCTTAACCTCCTCAATCACATTGAGGCTATTTCCAAAGATCAATATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.10% | 36.80% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 41.50% | 58.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 94.40% | 5.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 49.70% | 50.10% | 0.17% | 0.00% | NA |
| Indica II | 465 | 50.10% | 49.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 29.40% | 70.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 44.30% | 55.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 7.70% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 78.10% | 21.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 20.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209592277 | C -> A | LOC_Os12g16740.1 | missense_variant ; p.Leu421Ile; MODERATE | nonsynonymous_codon ; L421I | Average:44.014; most accessible tissue: Minghui63 young leaf, score: 67.374 | benign  |
0.629 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209592277 | 6.37E-06 | NA | mr1558 | 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 |
| vg1209592277 | 4.30E-06 | NA | mr1558 | 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 |
| vg1209592277 | 8.73E-06 | 4.32E-06 | mr1672 | 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 |