Search for Variation information by Variation ID:
Detailed information for vg1120089078:
| Variant ID: vg1120089078 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20089078 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
TCTTGTTCATGAGAGGGGGATTGAGATTACCCAAAGAAGTATCAATGCGATCAACAAGATTAAACCTCTGGAGGATAAAACAGAATTGCAGGAGATGATC[G/A]
GCAAGATTAATTTTGTTAGAAGACTTATTTCTAATTTGTCTGGAAGATTAGAGCCTTTTACGCCATTATTACGATTGAAGGCCGATGAGCAGTTCACTTG
Reverse complement sequence
CAAGTGAACTGCTCATCGGCCTTCAATCGTAATAATGGCGTAAAAGGCTCTAATCTTCCAGACAAATTAGAAATAAGTCTTCTAACAAAATTAATCTTGC[C/T]
GATCATCTCCTGCAATTCTGTTTTATCCTCCAGAGGTTTAATCTTGTTGATCGCATTGATACTTCTTTGGGTAATCTCAATCCCCCTCTCATGAACAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.50% | 6.50% | 0.21% | 0.87% | NA |
| All Indica | 2759 | 88.40% | 9.90% | 0.33% | 1.38% | NA |
| All Japonica | 1512 | 98.60% | 1.30% | 0.00% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 70.50% | 23.40% | 1.08% | 4.95% | NA |
| Indica III | 913 | 91.70% | 7.20% | 0.44% | 0.66% | NA |
| Indica Intermediate | 786 | 86.50% | 12.30% | 0.00% | 1.15% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 14.40% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120089078 | G -> A | LOC_Os11g34290.1 | missense_variant ; p.Gly1318Ser; MODERATE | nonsynonymous_codon ; G1318S | Average:31.816; most accessible tissue: Zhenshan97 young leaf, score: 43.23 | benign  |
0.398 |
DELETERIOUS | 0.04 |
| vg1120089078 | G -> DEL | LOC_Os11g34290.1 | N | frameshift_variant | Average:31.816; most accessible tissue: Zhenshan97 young leaf, score: 43.23 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120089078 | 1.27E-06 | 7.70E-13 | mr1183 | 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 |
| vg1120089078 | 4.21E-06 | 5.23E-08 | mr1183 | 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 |
| vg1120089078 | 2.68E-06 | NA | mr1503 | 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 |
| vg1120089078 | 6.62E-06 | 2.84E-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 |