Search for Variation information by Variation ID:
Detailed information for vg0211791834:
| Variant ID: vg0211791834 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 11791834 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
TGGTGCACATGGGTTATCTTTAGTGAAGCTTAAGATACCTATGCGAGTTCATACTCCTGGAGGTGGCATGACCACAACTCACTATTGCCCGTCAGTGAGA[G/A,T]
TTGAAATCCAAGGGTTGATTTTTCCAGCCAACCTCATTCTTCTCGAATCTAAGGATCTAGATGTTATTCTGGGAATGGATTGGCTAACAAGGCACAGAGG
Reverse complement sequence
CCTCTGTGCCTTGTTAGCCAATCCATTCCCAGAATAACATCTAGATCCTTAGATTCGAGAAGAATGAGGTTGGCTGGAAAAATCAACCCTTGGATTTCAA[C/T,A]
TCTCACTGACGGGCAATAGTGAGTTGTGGTCATGCCACCTCCAGGAGTATGAACTCGCATAGGTATCTTAAGCTTCACTAAAGATAACCCATGTGCACCA
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 | 57.60% | 39.20% | 2.14% | 1.10% | NA |
| All Indica | 2759 | 94.60% | 4.00% | 1.45% | 0.04% | NA |
| All Japonica | 1512 | 1.50% | 98.30% | 0.13% | 0.00% | NA |
| Aus | 269 | 19.70% | 44.60% | 20.82% | 14.87% | NA |
| Indica I | 595 | 93.30% | 4.50% | 2.18% | 0.00% | NA |
| Indica II | 465 | 95.70% | 3.40% | 0.65% | 0.22% | NA |
| Indica III | 913 | 96.10% | 3.10% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 93.10% | 4.80% | 2.04% | 0.00% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.40% | 97.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 0.00% | 88.50% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 38.90% | 57.80% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0211791834 | G -> A | LOC_Os02g20020.1 | missense_variant ; p.Val303Ile; MODERATE | nonsynonymous_codon ; V303I | Average:16.802; most accessible tissue: Callus, score: 30.5 | benign  |
-0.171 |
TOLERATED | 1.00 |
| vg0211791834 | G -> T | LOC_Os02g20020.1 | missense_variant ; p.Val303Phe; MODERATE | N | Average:16.802; most accessible tissue: Callus, score: 30.5 | N | N | N | N |
| vg0211791834 | G -> T | LOC_Os02g20030.1 | downstream_gene_variant ; 3997.0bp to feature; MODIFIER | N | Average:16.802; most accessible tissue: Callus, score: 30.5 | N | N | N | N |
| vg0211791834 | G -> DEL | LOC_Os02g20020.1 | N | frameshift_variant | Average:16.802; most accessible tissue: Callus, score: 30.5 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211791834 | NA | 4.50E-11 | mr1553 | 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 |
| vg0211791834 | NA | 7.96E-12 | mr1636 | 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 |
| vg0211791834 | NA | 3.12E-06 | mr1646 | 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 |
| vg0211791834 | NA | 1.16E-17 | mr1767 | 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 |
| vg0211791834 | NA | 2.23E-12 | mr1216_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 |
| vg0211791834 | 3.72E-07 | NA | mr1987_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 |