Search for Variation information by Variation ID:
Detailed information for vg0313958242:
| Variant ID: vg0313958242 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 13958242 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.59, T: 0.41, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
CAACATATATAAGCAGCAACTAGCGGAATTGCTAAATCTAAAATATATAAACTACGAGCTTACCTTTATTGATAAGTTCTTGTAAGGAATATGCAGCTCA[T/C]
ATGGTGTCCGCTGAGTGATGTCATCAACGGAACAGGTCGATTCGTCCTGTGTTTGCATGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCGCA
Reverse complement sequence
TGCGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCATGCAAACACAGGACGAATCGACCTGTTCCGTTGATGACATCACTCAGCGGACACCAT[A/G]
TGAGCTGCATATTCCTTACAAGAACTTATCAATAAAGGTAAGCTCGTAGTTTATATATTTTAGATTTAGCAATTCCGCTAGTTGCTGCTTATATATGTTG
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 | 66.30% | 33.60% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.60% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 13.00% | 87.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 63.90% | 36.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.60% | 3.20% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 22.40% | 77.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.40% | 97.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 46.70% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0313958242 | T -> C | LOC_Os03g24490.1 | missense_variant ; p.Tyr1386Cys; MODERATE | nonsynonymous_codon ; Y1386C | Average:8.311; most accessible tissue: Callus, score: 17.567 | benign  |
-0.233 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0313958242 | NA | 2.51E-12 | mr1648 | 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 |
| vg0313958242 | NA | 7.59E-07 | mr1648 | Jap_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 |
| vg0313958242 | NA | 9.78E-08 | mr1697 | Jap_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 |
| vg0313958242 | NA | 4.88E-06 | mr1510_2 | Jap_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 |