Search for Variation information by Variation ID:
Detailed information for vg0516129780:
| Variant ID: vg0516129780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 16129780 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTAATGCTGCGCCTTTAAGAGATGGACGAGATTGTCCTCTATTGCTTCCGGATACTTGTCGATCATTGAGACGTTTACTTTCCGAGGGTCGATGAATC[T/C]
AGTATCGAAAACCCCCCACCGTCGGGCCCTTTGAATCTCCATTCTACAACGATAAAAGGAAGTATATATTATATATGGTGTACTTATATACAAGGACCTA
Reverse complement sequence
TAGGTCCTTGTATATAAGTACACCATATATAATATATACTTCCTTTTATCGTTGTAGAATGGAGATTCAAAGGGCCCGACGGTGGGGGGTTTTCGATACT[A/G]
GATTCATCGACCCTCGGAAAGTAAACGTCTCAATGATCGACAAGTATCCGGAAGCAATAGAGGACAATCTCGTCCATCTCTTAAAGGCGCAGCATTACAA
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 | 44.40% | 9.50% | 22.64% | 23.49% | NA |
| All Indica | 2759 | 29.20% | 15.60% | 32.77% | 22.40% | NA |
| All Japonica | 1512 | 75.30% | 0.40% | 4.43% | 19.91% | NA |
| Aus | 269 | 4.50% | 3.70% | 29.00% | 62.83% | NA |
| Indica I | 595 | 30.80% | 3.40% | 37.82% | 28.07% | NA |
| Indica II | 465 | 17.20% | 20.00% | 32.47% | 30.32% | NA |
| Indica III | 913 | 28.40% | 24.60% | 31.22% | 15.77% | NA |
| Indica Intermediate | 786 | 36.10% | 11.80% | 30.92% | 21.12% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 2.22% | 4.82% | NA |
| Tropical Japonica | 504 | 46.00% | 1.00% | 8.33% | 44.64% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.40% | 3.32% | 16.18% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 53.30% | 2.20% | 21.11% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0516129780 | T -> DEL | LOC_Os05g27690.1 | N | frameshift_variant | Average:43.765; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0516129780 | T -> C | LOC_Os05g27690.1 | missense_variant ; p.Arg555Gly; MODERATE | nonsynonymous_codon ; R555G | Average:43.765; most accessible tissue: Zhenshan97 panicle, score: 59.59 | benign  |
-1.042 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0516129780 | NA | 1.80E-06 | mr1525 | 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 |
| vg0516129780 | NA | 3.87E-09 | mr1322_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 |
| vg0516129780 | NA | 3.01E-06 | mr1322_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 |
| vg0516129780 | 6.98E-06 | 4.68E-09 | mr1363_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 |
| vg0516129780 | 2.06E-06 | 4.64E-08 | mr1363_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 |