Search for Variation information by Variation ID:
Detailed information for vg0817496253:
| Variant ID: vg0817496253 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17496253 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACATATCATCTACCGATTTGGTATTCCCCAGACCATTACAACTGATCAAGGTTCGATCTTTGTGTCCGATGAGTTTGTTCAGTTTGCCGATAGCATGGG[C/T]
ATCAAGTTGTTAAATTCTTCCCCGTACTATGCGCAGGCTAACGGACAAACCGAGGCGTCTAACAAGAGTTTGCTCAAGTTGGTTAAGAGAAAGATTTCTG
Reverse complement sequence
CAGAAATCTTTCTCTTAACCAACTTGAGCAAACTCTTGTTAGACGCCTCGGTTTGTCCGTTAGCCTGCGCATAGTACGGGGAAGAATTTAACAACTTGAT[G/A]
CCCATGCTATCGGCAAACTGAACAAACTCATCGGACACAAAGATCGAACCTTGATCAGTTGTAATGGTCTGGGGAATACCAAATCGGTAGATGATATGTT
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 | 62.50% | 16.90% | 8.63% | 12.00% | NA |
| All Indica | 2759 | 49.20% | 22.30% | 10.29% | 18.19% | NA |
| All Japonica | 1512 | 83.30% | 9.90% | 5.95% | 0.93% | NA |
| Aus | 269 | 74.70% | 5.20% | 4.83% | 15.24% | NA |
| Indica I | 595 | 82.90% | 2.50% | 6.89% | 7.73% | NA |
| Indica II | 465 | 41.70% | 7.30% | 11.61% | 39.35% | NA |
| Indica III | 913 | 33.50% | 44.40% | 10.19% | 11.94% | NA |
| Indica Intermediate | 786 | 46.40% | 20.50% | 12.21% | 20.87% | NA |
| Temperate Japonica | 767 | 98.60% | 0.40% | 0.39% | 0.65% | NA |
| Tropical Japonica | 504 | 58.10% | 26.40% | 14.29% | 1.19% | NA |
| Japonica Intermediate | 241 | 87.10% | 5.40% | 6.22% | 1.24% | NA |
| VI/Aromatic | 96 | 78.10% | 5.20% | 14.58% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 15.60% | 7.78% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817496253 | C -> T | LOC_Os08g28630.1 | synonymous_variant ; p.Gly1305Gly; LOW | synonymous_codon | Average:12.542; most accessible tissue: Callus, score: 36.956 | N | N | N | N |
| vg0817496253 | C -> T | LOC_Os08g28630.1 | synonymous_variant ; p.Gly1305Gly; LOW | nonsynonymous_codon ; G1305A | Average:12.542; most accessible tissue: Callus, score: 36.956 | possibly damaging  |
1.526 |
DELETERIOUS | 0.00 |
| vg0817496253 | C -> DEL | LOC_Os08g28630.1 | N | frameshift_variant | Average:12.542; most accessible tissue: Callus, score: 36.956 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817496253 | 1.27E-06 | 4.95E-08 | mr1133 | 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 |
| vg0817496253 | NA | 3.71E-07 | mr1133_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 |
| vg0817496253 | NA | 8.56E-06 | mr1667_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 |