Search for Variation information by Variation ID:
Detailed information for vg0809848736:
| Variant ID: vg0809848736 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9848736 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 350. )
Flanking Sequence (100 bp) in Reference Genome:
AAAACGCGAGGATGACATCCTCATGAAAGCGTTGGGAAACGAAGAACACCATGGACGAACAAGGGGCATTGGCTCCAATGTTCCATGGAAGTTTGGGTTT[C/T]
CCCAATACGCGTGGCAGTACAAGAAGCACAAGCTTTCCAAGGCGCAGAAAGCTGCATGCATTAAGGCCCAACTTCGGGAGGAGCTTAAAGAAGAGCTTAG
Reverse complement sequence
CTAAGCTCTTCTTTAAGCTCCTCCCGAAGTTGGGCCTTAATGCATGCAGCTTTCTGCGCCTTGGAAAGCTTGTGCTTCTTGTACTGCCACGCGTATTGGG[G/A]
AAACCCAAACTTCCATGGAACATTGGAGCCAATGCCCCTTGTTCGTCCATGGTGTTCTTCGTTTCCCAACGCTTTCATGAGGATGTCATCCTCGCGTTTT
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 | 84.30% | 15.50% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 85.20% | 14.60% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 85.10% | 14.50% | 0.46% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.00% | 3.90% | 0.17% | 0.00% | NA |
| Indica II | 465 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 74.70% | 25.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 85.60% | 14.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 92.80% | 6.90% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 70.40% | 28.60% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.90% | 9.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 21.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0809848736 | C -> T | LOC_Os08g16160.1 | missense_variant ; p.Pro274Ser; MODERATE | nonsynonymous_codon ; P274S | Average:43.478; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | possibly damaging  |
1.731 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809848736 | NA | 2.02E-07 | mr1080 | 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 |
| vg0809848736 | 4.69E-06 | 1.67E-06 | mr1137 | 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 |
| vg0809848736 | NA | 2.90E-06 | mr1140 | 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 |
| vg0809848736 | NA | 5.36E-06 | mr1203 | 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 |
| vg0809848736 | NA | 9.79E-06 | mr1618 | 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 |
| vg0809848736 | NA | 5.17E-07 | mr1798_2 | 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 |