Search for Variation information by Variation ID:
Detailed information for vg1210713193:
| Variant ID: vg1210713193 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 10713193 |
| 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, T: 0.00, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
CTTGCACCAGAACATCCCACTTCAGGAGAGGTGTGCTGGTGAAGGTAGCCAGTTGGGTTGGTTTTAATCTTCCATGGTCGATCTGGTAATCTTTCTCTTT[C/T]
CCTTCTTCCTTTTTCAGATAATATGCGTTCCTTGTATGTATAATAACTCTGTAATAAACAAATGAACTGCCGAAATGAATAGCTATGTAGAATAATTATG
Reverse complement sequence
CATAATTATTCTACATAGCTATTCATTTCGGCAGTTCATTTGTTTATTACAGAGTTATTATACATACAAGGAACGCATATTATCTGAAAAAGGAAGAAGG[G/A]
AAAGAGAAAGATTACCAGATCGACCATGGAAGATTAAAACCAACCCAACTGGCTACCTTCACCAGCACACCTCTCCTGAAGTGGGATGTTCTGGTGCAAG
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 | 86.40% | 13.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 77.40% | 22.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 53.40% | 46.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 85.60% | 14.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 89.00% | 11.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 77.20% | 22.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1210713193 | C -> T | LOC_Os12g18530.1 | missense_variant ; p.Glu754Lys; MODERATE | nonsynonymous_codon ; E754K | Average:53.285; most accessible tissue: Callus, score: 80.465 | benign  |
1.029 |
TOLERATED | 0.10 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1210713193 | NA | 3.17E-06 | mr1100 | 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 |
| vg1210713193 | NA | 5.69E-08 | mr1164_2 | 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 |
| vg1210713193 | NA | 9.88E-06 | mr1170_2 | 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 |
| vg1210713193 | NA | 6.01E-09 | mr1220_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 |
| vg1210713193 | NA | 5.49E-06 | mr1308_2 | 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 |
| vg1210713193 | NA | 4.65E-06 | mr1361_2 | 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 |
| vg1210713193 | NA | 6.62E-08 | mr1864_2 | 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 |