Search for Variation information by Variation ID:
Detailed information for vg0610852694:
| Variant ID: vg0610852694 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10852694 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAAGGATGATCCGTGGGTTCTTGCTAAGCGTGTTGCTCAGGTTTTCTATGTCAATGATCCTTTCGACGATAAGATGGCCATTGCTGTACCGGGAAAGCAA[A/G]
ACATCATTGGCATTGATAGCATTGAAGACGCGTCAGATTACAACCAATACGACGACGTCCCTTTGTTCACAGATTTTCCTAACCGGATCAAGGAAGTTGA
Reverse complement sequence
TCAACTTCCTTGATCCGGTTAGGAAAATCTGTGAACAAAGGGACGTCGTCGTATTGGTTGTAATCTGACGCGTCTTCAATGCTATCAATGCCAATGATGT[T/C]
TTGCTTTCCCGGTACAGCAATGGCCATCTTATCGTCGAAAGGATCATTGACATAGAAAACCTGAGCAACACGCTTAGCAAGAACCCACGGATCATCCTTG
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 | 85.30% | 7.40% | 5.97% | 1.25% | NA |
| All Indica | 2759 | 75.20% | 12.70% | 10.04% | 2.10% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.13% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 59.30% | 21.30% | 11.26% | 8.07% | NA |
| Indica II | 465 | 85.60% | 9.00% | 5.38% | 0.00% | NA |
| Indica III | 913 | 77.20% | 10.00% | 12.27% | 0.55% | NA |
| Indica Intermediate | 786 | 78.60% | 11.50% | 9.29% | 0.64% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610852694 | A -> G | LOC_Os06g19080.1 | missense_variant ; p.Asn916Asp; MODERATE | nonsynonymous_codon | Average:19.173; most accessible tissue: Callus, score: 59.723 | benign  |
1.288 |
DELETERIOUS | 0.00 |
| vg0610852694 | A -> DEL | LOC_Os06g19080.1 | N | frameshift_variant | Average:19.173; most accessible tissue: Callus, score: 59.723 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610852694 | 3.89E-06 | 2.76E-06 | mr1708 | 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 |