Search for Variation information by Variation ID:
Detailed information for vg0817359828:
| Variant ID: vg0817359828 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17359828 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCCGCTCACCTATATTACTAATGATTTGTTTCGGCGGATGTCGTCATTGAATATGCAAAGGAACAGCGACTTCTGAAGTTGATTCACGTTCTGTATCAG[C/T]
ACTGGTCGAAGTTGTAATCTCTAGAGGACCATCTCGATCAGCATCAACAGTACCCGAACCCGACAAGCCTGGCCGGTCTGACCGCACCCCCTGTGGTGGT
Reverse complement sequence
ACCACCACAGGGGGTGCGGTCAGACCGGCCAGGCTTGTCGGGTTCGGGTACTGTTGATGCTGATCGAGATGGTCCTCTAGAGATTACAACTTCGACCAGT[G/A]
CTGATACAGAACGTGAATCAACTTCAGAAGTCGCTGTTCCTTTGCATATTCAATGACGACATCCGCCGAAACAAATCATTAGTAATATAGGTGAGCGGAC
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 | 34.80% | 8.50% | 1.74% | 54.93% | NA |
| All Indica | 2759 | 5.50% | 8.00% | 2.79% | 83.73% | NA |
| All Japonica | 1512 | 89.60% | 6.50% | 0.07% | 3.84% | NA |
| Aus | 269 | 1.10% | 27.90% | 1.49% | 69.52% | NA |
| Indica I | 595 | 7.90% | 3.20% | 2.35% | 86.55% | NA |
| Indica II | 465 | 9.90% | 6.50% | 2.58% | 81.08% | NA |
| Indica III | 913 | 2.00% | 15.00% | 3.40% | 79.63% | NA |
| Indica Intermediate | 786 | 5.10% | 4.50% | 2.54% | 87.91% | NA |
| Temperate Japonica | 767 | 94.80% | 4.30% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 83.30% | 7.70% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 86.30% | 10.80% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 91.70% | 1.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 55.60% | 6.70% | 0.00% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817359828 | C -> T | LOC_Os08g28450.1 | missense_variant ; p.Ala710Thr; MODERATE | nonsynonymous_codon ; A710T | Average:12.625; most accessible tissue: Callus, score: 32.286 | benign  |
-1.228 |
TOLERATED | 1.00 |
| vg0817359828 | C -> DEL | LOC_Os08g28450.1 | N | frameshift_variant | Average:12.625; most accessible tissue: Callus, score: 32.286 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817359828 | 1.78E-06 | 1.02E-06 | mr1344 | 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 |