Search for Variation information by Variation ID:
Detailed information for vg0714324691:
| Variant ID: vg0714324691 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14324691 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGATGACCAAATCCTTGTACCCGAGGATTGAAATTGACGCCATTGATGGCTTTGCAGACGGGACAAGCGAAGAGGCTGCTCTTGATCTTATCAACAAT[G/A]
CTCAAAACGCGGCTGACAGGATTGCAAGTGACGTTGTAGAGCAATTCCGCAACAACGACCTTCAGCCGAGTAACAATAACTCTGATGATGAAAGGACTGA
Reverse complement sequence
TCAGTCCTTTCATCATCAGAGTTATTGTTACTCGGCTGAAGGTCGTTGTTGCGGAATTGCTCTACAACGTCACTTGCAATCCTGTCAGCCGCGTTTTGAG[C/T]
ATTGTTGATAAGATCAAGAGCAGCCTCTTCGCTTGTCCCGTCTGCAAAGCCATCAATGGCGTCAATTTCAATCCTCGGGTACAAGGATTTGGTCATCGCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.00% | 4.40% | 60.33% | 3.32% | NA |
| All Indica | 2759 | 20.30% | 0.30% | 76.95% | 2.39% | NA |
| All Japonica | 1512 | 57.90% | 12.50% | 24.27% | 5.36% | NA |
| Aus | 269 | 11.50% | 0.00% | 85.13% | 3.35% | NA |
| Indica I | 595 | 39.20% | 0.20% | 56.47% | 4.20% | NA |
| Indica II | 465 | 24.30% | 0.90% | 72.69% | 2.15% | NA |
| Indica III | 913 | 5.00% | 0.10% | 93.43% | 1.42% | NA |
| Indica Intermediate | 786 | 21.50% | 0.40% | 75.83% | 2.29% | NA |
| Temperate Japonica | 767 | 74.80% | 1.80% | 13.04% | 10.30% | NA |
| Tropical Japonica | 504 | 34.30% | 32.10% | 33.53% | 0.00% | NA |
| Japonica Intermediate | 241 | 53.10% | 5.40% | 40.66% | 0.83% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 90.62% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 8.90% | 50.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714324691 | G -> DEL | LOC_Os07g25080.1 | N | frameshift_variant | Average:23.925; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| vg0714324691 | G -> A | LOC_Os07g25080.1 | missense_variant ; p.Ala796Thr; MODERATE | nonsynonymous_codon ; A796T | Average:23.925; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | possibly damaging  |
1.757 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714324691 | 4.27E-06 | 1.36E-08 | mr1471 | 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 |
| vg0714324691 | NA | 4.43E-07 | mr1642 | Jap_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 |