Search for Variation information by Variation ID:
Detailed information for vg0211446231:
| Variant ID: vg0211446231 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 11446231 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 115. )
Flanking Sequence (100 bp) in Reference Genome:
GACTCAATCTCTGGGAGAGAGTCGTTCAAGGCGAACCTTGCCCGCGAGAATGAGACTGAGAATTCATTCCCTCCCAAAGTTATCTTGAGGCTATCTAACC[G/A]
GGGCGTGTTTATTAGGAGTTGCTCAATGAGAAGCCCGATTAGAATGTCAAAATCTTGAATTTCAAAGACGTGGAAATCCAAGACTGCCTCCCTATCTTCA
Reverse complement sequence
TGAAGATAGGGAGGCAGTCTTGGATTTCCACGTCTTTGAAATTCAAGATTTTGACATTCTAATCGGGCTTCTCATTGAGCAACTCCTAATAAACACGCCC[C/T]
GGTTAGATAGCCTCAAGATAACTTTGGGAGGGAATGAATTCTCAGTCTCATTCTCGCGGGCAAGGTTCGCCTTGAACGACTCTCTCCCAGAGATTGAGTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.30% | 49.00% | 0.28% | 0.44% | NA |
| All Indica | 2759 | 73.00% | 26.10% | 0.18% | 0.72% | NA |
| All Japonica | 1512 | 2.60% | 97.00% | 0.46% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 70.30% | 28.90% | 0.17% | 0.67% | NA |
| Indica II | 465 | 67.10% | 32.00% | 0.22% | 0.65% | NA |
| Indica III | 913 | 79.40% | 20.00% | 0.33% | 0.22% | NA |
| Indica Intermediate | 786 | 71.00% | 27.60% | 0.00% | 1.40% | NA |
| Temperate Japonica | 767 | 0.10% | 99.20% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 3.80% | 96.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 7.90% | 91.30% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 27.10% | 71.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 33.30% | 65.60% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0211446231 | G -> A | LOC_Os02g19600.1 | missense_variant ; p.Arg177Trp; MODERATE | nonsynonymous_codon ; R177W | Average:46.131; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | probably damaging  |
3.299 |
DELETERIOUS | 0.00 |
| vg0211446231 | G -> DEL | LOC_Os02g19600.1 | N | frameshift_variant | Average:46.131; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211446231 | NA | 1.66E-08 | mr1172_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 |
| vg0211446231 | NA | 4.05E-07 | mr1623_2 | 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 |
| vg0211446231 | NA | 1.30E-07 | mr1783_2 | 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 |
| vg0211446231 | NA | 4.94E-07 | mr1785_2 | 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 |
| vg0211446231 | NA | 1.40E-17 | mr1874_2 | 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 |