Search for Variation information by Variation ID:
Detailed information for vg1212596614:
| Variant ID: vg1212596614 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12596614 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTAATTGGATAAATATAACCATAACGGGAGTAATTGTGTGTGAATGTTATGAATGAGTCATAGCCATCCATACTTTTCACAGGAAATGGATCACAAATAT[C/T]
TGTGTGAATGATTTCCAAAATTCCTGCGCTTCGTTTTGCACCCTTTTTGATGCTCTTTACAAACTTTCCTTTAATGCATTCTATGCATTGTTCTAAATCT
Reverse complement sequence
AGATTTAGAACAATGCATAGAATGCATTAAAGGAAAGTTTGTAAAGAGCATCAAAAAGGGTGCAAAACGAAGCGCAGGAATTTTGGAAATCATTCACACA[G/A]
ATATTTGTGATCCATTTCCTGTGAAAAGTATGGATGGCTATGACTCATTCATAACATTCACACACAATTACTCCCGTTATGGTTATATTTATCCAATTAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.00% | 0.70% | 0.68% | 39.63% | NA |
| All Indica | 2759 | 47.70% | 0.00% | 0.94% | 51.32% | NA |
| All Japonica | 1512 | 78.00% | 2.10% | 0.26% | 19.58% | NA |
| Aus | 269 | 78.80% | 0.00% | 0.00% | 21.19% | NA |
| Indica I | 595 | 28.90% | 0.00% | 2.69% | 68.40% | NA |
| Indica II | 465 | 53.50% | 0.00% | 0.22% | 46.24% | NA |
| Indica III | 913 | 51.70% | 0.00% | 0.66% | 47.65% | NA |
| Indica Intermediate | 786 | 53.90% | 0.00% | 0.38% | 45.67% | NA |
| Temperate Japonica | 767 | 76.40% | 3.90% | 0.39% | 19.30% | NA |
| Tropical Japonica | 504 | 86.90% | 0.00% | 0.20% | 12.90% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.80% | 0.00% | 34.44% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 0.00% | 76.04% | NA |
| Intermediate | 90 | 61.10% | 2.20% | 2.22% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212596614 | C -> DEL | LOC_Os12g22310.1 | N | frameshift_variant | Average:8.47; most accessible tissue: Callus, score: 28.519 | N | N | N | N |
| vg1212596614 | C -> T | LOC_Os12g22310.1 | missense_variant ; p.Asp280Asn; MODERATE | nonsynonymous_codon ; D280N | Average:8.47; most accessible tissue: Callus, score: 28.519 | benign  |
1.485 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212596614 | 1.63E-06 | NA | mr1124 | 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 |
| vg1212596614 | 8.53E-07 | 2.55E-06 | mr1134 | 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 |
| vg1212596614 | 7.65E-06 | 7.66E-06 | mr1861 | 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 |