Search for Variation information by Variation ID:
Detailed information for vg1010198226:
| Variant ID: vg1010198226 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10198226 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.30, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
ACTATCGATACCTCTTTGATTCTCCAACTGCAAGATCTACACCAAACCAAAAGATGTATTAGTATTTGAAAAAGAGAAACATAAATTTTGAGACTTACAT[A/G]
ATCTCTGAACCAATCAGGGAATTGTTCATTTTGCATGTTCTCAATGTTTTTTGGAGTTAGCCTTTTGCGTTTCTTCCTTTGCAAATCAGCAGCATGTTCT
Reverse complement sequence
AGAACATGCTGCTGATTTGCAAAGGAAGAAACGCAAAAGGCTAACTCCAAAAAACATTGAGAACATGCAAAATGAACAATTCCCTGATTGGTTCAGAGAT[T/C]
ATGTAAGTCTCAAAATTTATGTTTCTCTTTTTCAAATACTAATACATCTTTTGGTTTGGTGTAGATCTTGCAGTTGGAGAATCAAAGAGGTATCGATAGT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.70% | 2.60% | 54.40% | 20.27% | NA |
| All Indica | 2759 | 2.20% | 0.50% | 72.24% | 25.05% | NA |
| All Japonica | 1512 | 64.70% | 0.00% | 25.73% | 9.52% | NA |
| Aus | 269 | 0.40% | 40.50% | 40.89% | 18.22% | NA |
| Indica I | 595 | 1.30% | 0.50% | 73.95% | 24.20% | NA |
| Indica II | 465 | 2.40% | 0.00% | 58.49% | 39.14% | NA |
| Indica III | 913 | 2.50% | 0.00% | 81.16% | 16.32% | NA |
| Indica Intermediate | 786 | 2.40% | 1.40% | 68.70% | 27.48% | NA |
| Temperate Japonica | 767 | 86.60% | 0.00% | 7.69% | 5.74% | NA |
| Tropical Japonica | 504 | 36.30% | 0.00% | 51.59% | 12.10% | NA |
| Japonica Intermediate | 241 | 54.80% | 0.00% | 29.05% | 16.18% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 47.92% | 48.96% | NA |
| Intermediate | 90 | 32.20% | 1.10% | 36.67% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010198226 | A -> G | LOC_Os10g20280.1 | missense_variant&splice_region_variant ; p.Tyr702His; MODERATE | nonsynonymous_codon ; Y702H | Average:13.867; most accessible tissue: Callus, score: 35.639 | benign  |
-1.317 |
TOLERATED | 1.00 |
| vg1010198226 | A -> DEL | LOC_Os10g20280.1 | N | frameshift_variant | Average:13.867; most accessible tissue: Callus, score: 35.639 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010198226 | NA | 7.71E-06 | mr1209 | 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 |
| vg1010198226 | NA | 9.64E-09 | mr1275 | 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 |
| vg1010198226 | NA | 5.91E-09 | mr1078_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 |