Search for Variation information by Variation ID:
Detailed information for vg0318244684:
| Variant ID: vg0318244684 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18244684 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
TCTGCTTTGTCACTTTGTCAAAGAGATCAGTATTCTCGGGCCTGTGTACCTACACAACATGTTTCCTTTCGAGAGGTACATGGGCGTTCTGAAGAAGTAT[A/G]
TTCGTAACCGTGCTCGTCCAGAGGCAAGCATCGCCAAGGGGTATGGAACAGAGGAGGTCATCGAATTTTGCATAGAATTTATTGAAGACCTTCGCCCAAT
Reverse complement sequence
ATTGGGCGAAGGTCTTCAATAAATTCTATGCAAAATTCGATGACCTCCTCTGTTCCATACCCCTTGGCGATGCTTGCCTCTGGACGAGCACGGTTACGAA[T/C]
ATACTTCTTCAGAACGCCCATGTACCTCTCGAAAGGAAACATGTTGTGTAGGTACACAGGCCCGAGAATACTGATCTCTTTGACAAAGTGACAAAGCAGA
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 | 64.90% | 26.80% | 4.02% | 4.32% | NA |
| All Indica | 2759 | 56.90% | 30.80% | 5.44% | 6.92% | NA |
| All Japonica | 1512 | 84.90% | 14.60% | 0.33% | 0.13% | NA |
| Aus | 269 | 27.90% | 60.60% | 9.67% | 1.86% | NA |
| Indica I | 595 | 45.40% | 44.00% | 3.03% | 7.56% | NA |
| Indica II | 465 | 62.60% | 24.90% | 4.95% | 7.53% | NA |
| Indica III | 913 | 58.90% | 29.90% | 5.91% | 5.26% | NA |
| Indica Intermediate | 786 | 59.80% | 25.20% | 7.00% | 8.02% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 63.10% | 35.90% | 0.79% | 0.20% | NA |
| Japonica Intermediate | 241 | 83.00% | 16.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 18.80% | 5.21% | 1.04% | NA |
| Intermediate | 90 | 72.20% | 17.80% | 4.44% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318244684 | A -> DEL | LOC_Os03g31890.1 | N | frameshift_variant | Average:23.505; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0318244684 | A -> G | LOC_Os03g31890.1 | missense_variant ; p.Ile681Val; MODERATE | nonsynonymous_codon ; I681V | Average:23.505; most accessible tissue: Minghui63 panicle, score: 34.226 | benign  |
-0.686 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318244684 | 5.11E-07 | NA | mr1022 | 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 |