Search for Variation information by Variation ID:
Detailed information for vg0429946123:
| Variant ID: vg0429946123 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 29946123 |
| 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: 304. )
Flanking Sequence (100 bp) in Reference Genome:
GATCTTGGCTAAAAGAGAGATAGCTGAAAGCTCCTTCTGTTGGAAGGTTCTGCGATTCCTTTCGCTCCATATCTCCCAGGCGACCAACAACATCAAAGTG[C/T]
GGAGTGCCTTCTTAGATGTCTCTTGTATGTTTGCGGTAGCCTCCCACCAATCTAGCACCGTTGAAGTTTGCCGCCATTGGCTAGGATTTTGTTGCTCGCA
Reverse complement sequence
TGCGAGCAACAAAATCCTAGCCAATGGCGGCAAACTTCAACGGTGCTAGATTGGTGGGAGGCTACCGCAAACATACAAGAGACATCTAAGAAGGCACTCC[G/A]
CACTTTGATGTTGTTGGTCGCCTGGGAGATATGGAGCGAAAGGAATCGCAGAACCTTCCAACAGAAGGAGCTTTCAGCTATCTCTCTTTTAGCCAAGATC
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 | 89.40% | 10.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 82.70% | 17.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.30% | 9.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 52.60% | 47.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 20.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0429946123 | C -> T | LOC_Os04g50188.1 | missense_variant ; p.Arg56His; MODERATE | nonsynonymous_codon ; R56H | Average:52.612; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | probably damaging  |
2.33 |
TOLERATED | 0.15 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0429946123 | NA | 1.32E-06 | mr1082 | 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 |
| vg0429946123 | NA | 8.87E-06 | mr1890 | Jap_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 |