Search for Variation information by Variation ID:
Detailed information for vg0100095775:
| Variant ID: vg0100095775 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 95775 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
Flanking Sequence (100 bp) in Reference Genome:
TTCTGAATTTCTTCTCTTGGTCTTGAATTTCTACGGCCTTTCCTTGCTCCATTTGAACCCCAATTCCATCGCCTTCCTCAGTATCTTTTCGCATCTTTGT[G/A]
AGGCCTACATTGGGGTAGAGCCGTTTCTTGACCTCTTCCGCTTTTACTATGAGTTGCGCTGGATGGAACCTAAAAAGGTGTCCGGGTGTGTCGGTTTCCG
Reverse complement sequence
CGGAAACCGACACACCCGGACACCTTTTTAGGTTCCATCCAGCGCAACTCATAGTAAAAGCGGAAGAGGTCAAGAAACGGCTCTACCCCAATGTAGGCCT[C/T]
ACAAAGATGCGAAAAGATACTGAGGAAGGCGATGGAATTGGGGTTCAAATGGAGCAAGGAAAGGCCGTAGAAATTCAAGACCAAGAGAAGAAATTCAGAA
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 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 31.20% | 68.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 81.20% | 18.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100095775 | G -> A | LOC_Os01g01200.1 | missense_variant ; p.Glu93Lys; MODERATE | nonsynonymous_codon ; E93K | Average:50.426; most accessible tissue: Minghui63 panicle, score: 66.554 | benign  |
0.647 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100095775 | 1.03E-07 | NA | mr1134 | 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 |
| vg0100095775 | 7.74E-12 | NA | mr1134_2 | 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 |
| vg0100095775 | NA | 1.27E-09 | mr1166_2 | 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 |
| vg0100095775 | NA | 1.50E-08 | mr1567_2 | 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 |
| vg0100095775 | NA | 3.48E-07 | mr1582_2 | 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 |