Search for Variation information by Variation ID:
Detailed information for vg1124078354:
| Variant ID: vg1124078354 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24078354 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, A: 0.13, others allele: 0.00, population size: 39. )
Flanking Sequence (100 bp) in Reference Genome:
AGCACCTTGTTGCAATATGTTTCCACTCAGATTTAGACCATGCGTACCTTGAACAAGAGCTTTCTGCGCCTCTTTCATAAGCTTGTTGTATATGCTCTGC[C/A]
AGGAGTGACAATCACTGAGCATTTCATGAGCACACTGAACAGCATCTTGAAAGGCCTTCTTGGACATCAAAATGGTTTCTGGGAGCAGTTTGGGCTTTGA
Reverse complement sequence
TCAAAGCCCAAACTGCTCCCAGAAACCATTTTGATGTCCAAGAAGGCCTTTCAAGATGCTGTTCAGTGTGCTCATGAAATGCTCAGTGATTGTCACTCCT[G/T]
GCAGAGCATATACAACAAGCTTATGAAAGAGGCGCAGAAAGCTCTTGTTCAAGGTACGCATGGTCTAAATCTGAGTGGAAACATATTGCAACAAGGTGCT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.00% | 18.50% | 1.27% | 42.23% | NA |
| All Indica | 2759 | 9.40% | 27.60% | 1.92% | 61.11% | NA |
| All Japonica | 1512 | 86.00% | 1.10% | 0.33% | 12.50% | NA |
| Aus | 269 | 51.30% | 17.10% | 0.37% | 31.23% | NA |
| Indica I | 595 | 5.50% | 2.90% | 2.35% | 89.24% | NA |
| Indica II | 465 | 7.50% | 23.40% | 2.15% | 66.88% | NA |
| Indica III | 913 | 11.00% | 45.60% | 1.20% | 42.28% | NA |
| Indica Intermediate | 786 | 11.50% | 28.00% | 2.29% | 58.27% | NA |
| Temperate Japonica | 767 | 92.20% | 0.70% | 0.13% | 7.04% | NA |
| Tropical Japonica | 504 | 86.30% | 1.20% | 0.40% | 12.10% | NA |
| Japonica Intermediate | 241 | 66.00% | 2.50% | 0.83% | 30.71% | NA |
| VI/Aromatic | 96 | 61.50% | 26.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 43.30% | 27.80% | 1.11% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124078354 | C -> A | LOC_Os11g40390.1 | missense_variant ; p.Trp281Leu; MODERATE | nonsynonymous_codon ; W281F | Average:16.671; most accessible tissue: Callus, score: 61.174 | probably damaging  |
-2.577 |
TOLERATED | 1.00 |
| vg1124078354 | C -> A | LOC_Os11g40390.1 | missense_variant ; p.Trp281Leu; MODERATE | nonsynonymous_codon ; W281L | Average:16.671; most accessible tissue: Callus, score: 61.174 | possibly damaging |
-1.631 |
TOLERATED | 0.70 |
| vg1124078354 | C -> DEL | LOC_Os11g40390.1 | N | frameshift_variant | Average:16.671; most accessible tissue: Callus, score: 61.174 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124078354 | 5.30E-06 | NA | mr1133 | 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 |
| vg1124078354 | 1.76E-07 | 2.52E-08 | mr1133 | 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 |
| vg1124078354 | NA | 8.73E-06 | mr1395 | 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 |
| vg1124078354 | NA | 8.24E-06 | mr1133_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 |