Search for Variation information by Variation ID:
Detailed information for vg1110033540:
| Variant ID: vg1110033540 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10033540 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGTCACCTAAGACCGAGTCACAAATCGGTCATGTGGATGTTGGAAAAGATGATGACAATGTCTTGCAGGATAGTGGTGAAATAGAATCCAAAGTAGCTAT[A/G]
CATACATATCAAAGGCCGTATCCTGAACATATAGATTCGGTCCCGTACCCGCAAGGATTTGAAGTGCCCAACTTCACAAAATTCACAGGTGAGGATGCTA
Reverse complement sequence
TAGCATCCTCACCTGTGAATTTTGTGAAGTTGGGCACTTCAAATCCTTGCGGGTACGGGACCGAATCTATATGTTCAGGATACGGCCTTTGATATGTATG[T/C]
ATAGCTACTTTGGATTCTATTTCACCACTATCCTGCAAGACATTGTCATCATCTTTTCCAACATCCACATGACCGATTTGTGACTCGGTCTTAGGTGACA
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 | 63.10% | 4.50% | 17.01% | 15.45% | NA |
| All Indica | 2759 | 54.50% | 2.60% | 24.72% | 18.16% | NA |
| All Japonica | 1512 | 82.70% | 4.00% | 2.45% | 10.78% | NA |
| Aus | 269 | 55.80% | 0.70% | 26.77% | 16.73% | NA |
| Indica I | 595 | 58.50% | 6.60% | 21.68% | 13.28% | NA |
| Indica II | 465 | 49.50% | 0.20% | 28.82% | 21.51% | NA |
| Indica III | 913 | 52.10% | 0.20% | 26.73% | 20.92% | NA |
| Indica Intermediate | 786 | 57.10% | 3.90% | 22.26% | 16.67% | NA |
| Temperate Japonica | 767 | 74.30% | 4.80% | 3.78% | 17.08% | NA |
| Tropical Japonica | 504 | 95.20% | 2.80% | 1.19% | 0.79% | NA |
| Japonica Intermediate | 241 | 83.40% | 4.10% | 0.83% | 11.62% | NA |
| VI/Aromatic | 96 | 22.90% | 70.80% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 60.00% | 8.90% | 12.22% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1110033540 | A -> DEL | LOC_Os11g17890.1 | N | frameshift_variant | Average:11.639; most accessible tissue: Callus, score: 22.04 | N | N | N | N |
| vg1110033540 | A -> G | LOC_Os11g17890.1 | missense_variant ; p.Ile430Met; MODERATE | nonsynonymous_codon ; I430M | Average:11.639; most accessible tissue: Callus, score: 22.04 | benign  |
-0.697 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110033540 | 3.77E-06 | NA | mr1247 | 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 |
| vg1110033540 | 1.66E-07 | NA | mr1917 | 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 |