Search for Variation information by Variation ID:
Detailed information for vg0117058038:
| Variant ID: vg0117058038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 17058038 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CGCTTGGCCTTGCTGGCGCCTCGGCTTTGGGCATTTATCCGCAAAGTGCCCATGCTCGAAGCAGTTGAAGCACAGACGCTGCTGACCTTGAACGTCCCTG[C/T]
GGCCTTGACCAGGCTGCACGGCTGGCGTAGGGGGACGGGGCGCACGAGTCCCTTGCTGACTCTGCTGTTGCTGCGGCTGTGGGATGCGCACCACGAATTG
Reverse complement sequence
CAATTCGTGGTGCGCATCCCACAGCCGCAGCAACAGCAGAGTCAGCAAGGGACTCGTGCGCCCCGTCCCCCTACGCCAGCCGTGCAGCCTGGTCAAGGCC[G/A]
CAGGGACGTTCAAGGTCAGCAGCGTCTGTGCTTCAACTGCTTCGAGCATGGGCACTTTGCGGATAAATGCCCAAAGCCGAGGCGCCAGCAAGGCCAAGCG
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 | 72.70% | 11.60% | 10.98% | 4.68% | NA |
| All Indica | 2759 | 55.60% | 19.30% | 17.29% | 7.79% | NA |
| All Japonica | 1512 | 98.90% | 0.10% | 0.86% | 0.13% | NA |
| Aus | 269 | 89.60% | 0.40% | 8.92% | 1.12% | NA |
| Indica I | 595 | 70.60% | 1.20% | 17.14% | 11.09% | NA |
| Indica II | 465 | 47.30% | 39.10% | 10.54% | 3.01% | NA |
| Indica III | 913 | 49.90% | 24.40% | 18.73% | 6.90% | NA |
| Indica Intermediate | 786 | 55.70% | 15.40% | 19.72% | 9.16% | NA |
| Temperate Japonica | 767 | 99.30% | 0.30% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 1.79% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 12.20% | 4.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0117058038 | C -> T | LOC_Os01g31190.1 | missense_variant ; p.Arg114His; MODERATE | nonsynonymous_codon ; R114H | Average:22.158; most accessible tissue: Minghui63 panicle, score: 34.226 | probably damaging  |
2.568 |
DELETERIOUS | 0.04 |
| vg0117058038 | C -> DEL | LOC_Os01g31190.1 | N | frameshift_variant | Average:22.158; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0117058038 | 1.24E-07 | 8.09E-08 | mr1632 | Ind_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 |
| vg0117058038 | NA | 9.26E-08 | mr1039_2 | Ind_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 |
| vg0117058038 | NA | 7.22E-07 | mr1632_2 | Ind_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 |