Search for Variation information by Variation ID:
Detailed information for vg0100036866:
| Variant ID: vg0100036866 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36866 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CACATATTACTAGCATTCCGCATGTCAAATAACTTTTTTTTTAATATTGCAGTTATATTGCTGGGAGTGAATCCGAAGGTCATTTTGCATTGATAAACAA[G/C]
GCTTACTCTATGTAAGACTTGGGATTTTGACCCTGTCTCAATCTCTATTTAAATAGAATATATAGACAATAATTGGTCACCATGTTTTCCAATAGGAGGG
Reverse complement sequence
CCCTCCTATTGGAAAACATGGTGACCAATTATTGTCTATATATTCTATTTAAATAGAGATTGAGACAGGGTCAAAATCCCAAGTCTTACATAGAGTAAGC[C/G]
TTGTTTATCAATGCAAAATGACCTTCGGATTCACTCCCAGCAATATAACTGCAATATTAAAAAAAAAGTTATTTGACATGCGGAATGCTAGTAATATGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 1.20% | 2.75% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.10% | 0.98% | 0.00% | NA |
| All Japonica | 1512 | 89.70% | 3.50% | 6.75% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.00% | 1.18% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.00% | 1.94% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.30% | 0.30% | 1.40% | 0.00% | NA |
| Temperate Japonica | 767 | 83.30% | 5.60% | 11.08% | 0.00% | NA |
| Tropical Japonica | 504 | 97.00% | 2.00% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100036866 | G -> C | LOC_Os01g01080.1 | missense_variant ; p.Lys148Asn; MODERATE | nonsynonymous_codon ; K148N | Average:56.878; most accessible tissue: Zhenshan97 root, score: 77.09 | possibly damaging  |
1.635 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100036866 | 4.07E-06 | NA | mr1911_2 | 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 |