Search for Variation information by Variation ID:
Detailed information for vg0220796044:
| Variant ID: vg0220796044 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20796044 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
TTTTTGTGTGCCAAATATATGTCGATGACATTATATTTGGTTCTACTAACAAGTCTTTTAGTGAAGAGTTTAGTAGAATGATGACCAAGCGTTTTGAGAT[G/A]
TCCATGATGGGTGAATTGAAGTTCTTCCTCGGCCTTCAAATCAAGCAACTCAAGGAAGGAACTTTCATTTGCCAAATAAAGTATTTGAAGGACATGCTCA
Reverse complement sequence
TGAGCATGTCCTTCAAATACTTTATTTGGCAAATGAAAGTTCCTTCCTTGAGTTGCTTGATTTGAAGGCCGAGGAAGAACTTCAATTCACCCATCATGGA[C/T]
ATCTCAAAACGCTTGGTCATCATTCTACTAAACTCTTCACTAAAAGACTTGTTAGTAGAACCAAATATAATGTCATCGACATATATTTGGCACACAAAAA
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 | 53.40% | 46.30% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 86.90% | 12.70% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 1.10% | 98.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 30.90% | 68.80% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.30% | 1.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 69.20% | 30.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.20% | 11.40% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 87.30% | 12.10% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 28.90% | 71.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220796044 | G -> A | LOC_Os02g34670.1 | missense_variant ; p.Met153Ile; MODERATE | nonsynonymous_codon ; M153I | Average:13.017; most accessible tissue: Callus, score: 29.03 | benign  |
0.42 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220796044 | NA | 3.45E-07 | mr1162 | 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 |
| vg0220796044 | NA | 9.68E-12 | mr1281 | 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 |
| vg0220796044 | NA | 2.68E-10 | mr1342 | 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 |
| vg0220796044 | NA | 1.38E-19 | mr1598 | 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 |
| vg0220796044 | NA | 1.61E-07 | mr1748 | 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 |
| vg0220796044 | NA | 5.39E-07 | mr1785 | 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 |