Search for Variation information by Variation ID:
Detailed information for vg1126091011:
| Variant ID: vg1126091011 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26091011 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.34, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
GATGTCGCGGACCTGCTTCATCCAGGCGCGGAGCTGGTCGTCGTGGTTGGTCGTCTTGGTGACGTGCACCAGGAAGCCGTTCATGCTGTCCATCTCGTCC[C/T]
TGATGAACTGGATGTCGCCCTCCACGCCTCCCAGCAGCTTCGCCTCGTCCTTCACCACCTTCGACAACACACCCAGCAGCGACCCCACGGCGCCCAGCGT
Reverse complement sequence
ACGCTGGGCGCCGTGGGGTCGCTGCTGGGTGTGTTGTCGAAGGTGGTGAAGGACGAGGCGAAGCTGCTGGGAGGCGTGGAGGGCGACATCCAGTTCATCA[G/A]
GGACGAGATGGACAGCATGAACGGCTTCCTGGTGCACGTCACCAAGACGACCAACCACGACGACCAGCTCCGCGCCTGGATGAAGCAGGTCCGCGACATC
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 | 50.80% | 47.20% | 1.10% | 0.93% | NA |
| All Indica | 2759 | 32.00% | 67.30% | 0.62% | 0.00% | NA |
| All Japonica | 1512 | 87.80% | 7.30% | 2.05% | 2.91% | NA |
| Aus | 269 | 45.00% | 54.30% | 0.74% | 0.00% | NA |
| Indica I | 595 | 33.90% | 65.20% | 0.84% | 0.00% | NA |
| Indica II | 465 | 35.90% | 63.00% | 1.08% | 0.00% | NA |
| Indica III | 913 | 23.00% | 76.80% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 38.80% | 60.60% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 98.20% | 1.40% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 77.40% | 12.50% | 3.37% | 6.75% | NA |
| Japonica Intermediate | 241 | 76.30% | 14.90% | 4.98% | 3.73% | NA |
| VI/Aromatic | 96 | 19.80% | 79.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 44.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1126091011 | C -> T | LOC_Os11g43250.1 | missense_variant ; p.Arg38Lys; MODERATE | nonsynonymous_codon ; R38K | Average:68.805; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | benign  |
-0.392 |
TOLERATED | 1.00 |
| vg1126091011 | C -> DEL | LOC_Os11g43250.1 | N | frameshift_variant | Average:68.805; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126091011 | 5.92E-07 | 5.92E-07 | mr1526 | 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 |