Search for Variation information by Variation ID:
Detailed information for vg0416189113:
| Variant ID: vg0416189113 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16189113 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAGGAGTAACATTTGCAGTATAAATATAACAATGAGGGAGTAAACGCTACTAAACGTACAGCTTTTTTTGTGTGATCAATTCGGTATTGGCCATCATCC[T/C]
CCACATGAATCTCAAACTCCTTGAAGGTTTTTAACAGTGCACTGTAGAACTTCTTAATGTATTCTGGTAGGAATGCGGTAGCGCTCTCATCCCATCTGCA
Reverse complement sequence
TGCAGATGGGATGAGAGCGCTACCGCATTCCTACCAGAATACATTAAGAAGTTCTACAGTGCACTGTTAAAAACCTTCAAGGAGTTTGAGATTCATGTGG[A/G]
GGATGATGGCCAATACCGAATTGATCACACAAAAAAAGCTGTACGTTTAGTAGCGTTTACTCCCTCATTGTTATATTTATACTGCAAATGTTACTCCTGT
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 | 93.60% | 6.30% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 94.10% | 5.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 90.80% | 9.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.10% | 9.60% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 74.60% | 25.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0416189113 | T -> C | LOC_Os04g27400.1 | missense_variant ; p.Glu313Gly; MODERATE | nonsynonymous_codon ; E313G | Average:32.601; most accessible tissue: Zhenshan97 young leaf, score: 58.398 | possibly damaging  |
1.567 |
TOLERATED | 0.13 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416189113 | 1.32E-06 | 7.96E-07 | mr1925 | 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 |
| vg0416189113 | 6.28E-08 | 1.69E-09 | mr1498_2 | Jap_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 |
| vg0416189113 | 5.33E-06 | 5.33E-06 | mr1925_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 |