Search for Variation information by Variation ID:
Detailed information for vg0114134418:
| Variant ID: vg0114134418 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14134418 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCCGGTTCGATCAGAAAACGCTTATCAACTTGTGCGCGGACTTGTGCCGGTTCATTCGTCGCGACATCTGCAATCATCTAGGAGAGTTCCATGATCCTC[A/G]
TAGCGAACTTGCTACGGACCCCAAATTCAAGAATCTAAGAGAGTGGGAGAGGCAACATGCTGTGGACTAAATGGATGTATTTGTCGCGGGGGATACTTGT
Reverse complement sequence
ACAAGTATCCCCCGCGACAAATACATCCATTTAGTCCACAGCATGTTGCCTCTCCCACTCTCTTAGATTCTTGAATTTGGGGTCCGTAGCAAGTTCGCTA[T/C]
GAGGATCATGGAACTCTCCTAGATGATTGCAGATGTCGCGACGAATGAACCGGCACAAGTCCGCGCACAAGTTGATAAGCGTTTTCTGATCGAACCGGCT
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 | 47.20% | 14.00% | 13.03% | 25.75% | NA |
| All Indica | 2759 | 21.70% | 20.50% | 19.72% | 38.13% | NA |
| All Japonica | 1512 | 95.40% | 0.00% | 0.00% | 4.63% | NA |
| Aus | 269 | 31.60% | 34.20% | 22.68% | 11.52% | NA |
| Indica I | 595 | 9.60% | 8.20% | 14.45% | 67.73% | NA |
| Indica II | 465 | 9.70% | 27.70% | 22.80% | 39.78% | NA |
| Indica III | 913 | 36.50% | 24.50% | 17.74% | 21.25% | NA |
| Indica Intermediate | 786 | 20.70% | 20.70% | 24.17% | 34.35% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 89.70% | 0.00% | 0.00% | 10.32% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 55.20% | 0.00% | 2.08% | 42.71% | NA |
| Intermediate | 90 | 56.70% | 7.80% | 10.00% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114134418 | A -> G | LOC_Os01g25060.1 | missense_variant ; p.His794Arg; MODERATE | nonsynonymous_codon ; H794R | Average:25.032; most accessible tissue: Minghui63 root, score: 40.262 | possibly damaging  |
1.614 |
DELETERIOUS | 0.02 |
| vg0114134418 | A -> DEL | LOC_Os01g25060.1 | N | frameshift_variant | Average:25.032; most accessible tissue: Minghui63 root, score: 40.262 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114134418 | 2.38E-06 | 7.33E-06 | mr1324 | 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 |
| vg0114134418 | 3.72E-06 | 3.72E-06 | mr1420 | 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 |
| vg0114134418 | 5.47E-06 | 1.42E-08 | mr1764 | 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 |