Search for Variation information by Variation ID:
Detailed information for vg0809843322:
| Variant ID: vg0809843322 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9843322 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
TGGTAAGAAAGAACTTGGGTCTTCCCCTGCGGATTTGTCCGGAGATCAGGTACACAACATGGTGAAGGACATTACTAATGAGTTTGGGAAGAAAAGAAAA[C/T]
GTAGCAAGGAGGACAAGAAGAGGATGTGGAAGAAAAAATCCATATTTTGGCGGCTACCTTTTTGGGAAGATCTTGAGGTCCGTCATTGCATTGATCTGAT
Reverse complement sequence
ATCAGATCAATGCAATGACGGACCTCAAGATCTTCCCAAAAAGGTAGCCGCCAAAATATGGATTTTTTCTTCCACATCCTCTTCTTGTCCTCCTTGCTAC[G/A]
TTTTCTTTTCTTCCCAAACTCATTAGTAATGTCCTTCACCATGTTGTGTACCTGATCTCCGGACAAATCCGCAGGGGAAGACCCAAGTTCTTTCTTACCA
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 | 52.60% | 47.20% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 31.40% | 68.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 89.40% | 10.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 46.10% | 53.50% | 0.37% | 0.00% | NA |
| Indica I | 595 | 17.30% | 82.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 52.90% | 46.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 31.50% | 68.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 29.10% | 70.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 36.70% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0809843322 | C -> T | LOC_Os08g16140.1 | missense_variant ; p.Arg439Cys; MODERATE | nonsynonymous_codon ; R439C | Average:32.746; most accessible tissue: Minghui63 young leaf, score: 57.221 | benign  |
0.132 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809843322 | NA | 7.33E-06 | mr1075 | 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 |
| vg0809843322 | NA | 8.73E-08 | mr1183 | 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 |
| vg0809843322 | NA | 3.21E-06 | mr1441 | 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 |
| vg0809843322 | NA | 9.85E-07 | mr1503 | 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 |
| vg0809843322 | NA | 6.39E-11 | mr1510 | 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 |