Search for Variation information by Variation ID:
Detailed information for vg0129717929:
| Variant ID: vg0129717929 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 29717929 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
GGGTCTGGTCACGCCGCCTGGTGACCTAGGCTTTGATGCCTTGGCTGTGGTAGCCAATGGCCATGTACAGCAGAACGCCAACGCTAGTGCTCTAGCCGCT[G/T]
CTAGAACATTGCTGCCCAATGCTCCTCTTCCGGCGGCAATGGAGTTCAACCTTCCTGTTCTTCAAGTGCAAAGGTATTGGCTGCACTGGATTTCTGTTTT
Reverse complement sequence
AAAACAGAAATCCAGTGCAGCCAATACCTTTGCACTTGAAGAACAGGAAGGTTGAACTCCATTGCCGCCGGAAGAGGAGCATTGGGCAGCAATGTTCTAG[C/A]
AGCGGCTAGAGCACTAGCGTTGGCGTTCTGCTGTACATGGCCATTGGCTACCACAGCCAAGGCATCAAAGCCTAGGTCACCAGGCGGCGTGACCAGACCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.50% | 5.90% | 2.26% | 43.40% | NA |
| All Indica | 2759 | 36.20% | 9.20% | 3.59% | 51.00% | NA |
| All Japonica | 1512 | 78.80% | 0.00% | 0.07% | 21.16% | NA |
| Aus | 269 | 17.50% | 5.90% | 1.12% | 75.46% | NA |
| Indica I | 595 | 32.90% | 11.60% | 7.90% | 47.56% | NA |
| Indica II | 465 | 41.30% | 5.80% | 1.72% | 51.18% | NA |
| Indica III | 913 | 35.70% | 8.70% | 2.30% | 53.34% | NA |
| Indica Intermediate | 786 | 36.10% | 10.20% | 2.93% | 50.76% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 41.50% | 0.00% | 0.00% | 58.53% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.00% | 0.41% | 9.13% | NA |
| VI/Aromatic | 96 | 6.20% | 2.10% | 2.08% | 89.58% | NA |
| Intermediate | 90 | 53.30% | 5.60% | 2.22% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0129717929 | G -> T | LOC_Os01g51680.1 | missense_variant ; p.Ala51Ser; MODERATE | nonsynonymous_codon ; A51S | Average:23.144; most accessible tissue: Callus, score: 61.387 | benign  |
0.983 |
TOLERATED | 0.37 |
| vg0129717929 | G -> DEL | LOC_Os01g51680.1 | N | frameshift_variant | Average:23.144; most accessible tissue: Callus, score: 61.387 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0129717929 | 1.87E-06 | NA | mr1189_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 |
| vg0129717929 | 4.95E-07 | NA | mr1722_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 |
| vg0129717929 | 1.55E-06 | NA | mr1722_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 |