Search for Variation information by Variation ID:
Detailed information for vg1101210653:
| Variant ID: vg1101210653 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1210653 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TACCAAAATAAAACCTAATTAGCAAGCCATATGATTCAATCCATAAGTTTTCTTTTGCTCCTAGTGCCCATTGCAGGACTCTTATTTTTGCTCCTTGTGC[T/A]
CATAGCTGGGCTACCAGGAGTACTAGAACATGATGGCTTTCCCTTTGTCTTGCTCTTGGTCATTTTTGGTGCAACTGTAGGTGTTTCCTCCCCCAGACAT
Reverse complement sequence
ATGTCTGGGGGAGGAAACACCTACAGTTGCACCAAAAATGACCAAGAGCAAGACAAAGGGAAAGCCATCATGTTCTAGTACTCCTGGTAGCCCAGCTATG[A/T]
GCACAAGGAGCAAAAATAAGAGTCCTGCAATGGGCACTAGGAGCAAAAGAAAACTTATGGATTGAATCATATGGCTTGCTAATTAGGTTTTATTTTGGTA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.60% | 0.10% | 1.29% | 18.01% | NA |
| All Indica | 2759 | 69.20% | 0.30% | 2.07% | 28.52% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.13% | 1.46% | NA |
| Aus | 269 | 91.80% | 0.00% | 0.74% | 7.43% | NA |
| Indica I | 595 | 75.00% | 0.00% | 1.18% | 23.87% | NA |
| Indica II | 465 | 48.00% | 1.50% | 3.66% | 46.88% | NA |
| Indica III | 913 | 72.60% | 0.00% | 1.75% | 25.63% | NA |
| Indica Intermediate | 786 | 73.30% | 0.00% | 2.16% | 24.55% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.26% | 1.43% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 0.00% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101210653 | T -> A | LOC_Os11g03280.1 | missense_variant ; p.Ser874Cys; MODERATE | nonsynonymous_codon ; S874C | Average:25.916; most accessible tissue: Zhenshan97 panicle, score: 54.901 | possibly damaging  |
1.926 |
DELETERIOUS | 0.04 |
| vg1101210653 | T -> DEL | LOC_Os11g03280.1 | N | frameshift_variant | Average:25.916; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1101210653 | 3.50E-07 | 3.50E-07 | mr1584_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 |