Search for Variation information by Variation ID:
Detailed information for vg0522020155:
| Variant ID: vg0522020155 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22020155 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 209. )
Flanking Sequence (100 bp) in Reference Genome:
TTGGTATGAACCCTTCGGCTTGTTGTTGTTGGGCTTGTTGTTGTTGATCTTCTCACCATCTTTGTCTTCTCTTTTGCCTCTCCCAAGCTTAGAACAATGC[G/A]
AACGAAGATGATCAATTGAACCACATTCAAAGCAATGATTTGGACCACCTCTTTTCCAGTTCCTGGCATTATTCATAGCTCGAGCAATTCTGTTAGCAAC
Reverse complement sequence
GTTGCTAACAGAATTGCTCGAGCTATGAATAATGCCAGGAACTGGAAAAGAGGTGGTCCAAATCATTGCTTTGAATGTGGTTCAATTGATCATCTTCGTT[C/T]
GCATTGTTCTAAGCTTGGGAGAGGCAAAAGAGAAGACAAAGATGGTGAGAAGATCAACAACAACAAGCCCAACAACAACAAGCCGAAGGGTTCATACCAA
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 | 60.60% | 39.30% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 96.90% | 2.90% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 1.10% | 98.70% | 0.13% | 0.00% | NA |
| Aus | 269 | 47.20% | 52.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.20% | 2.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.30% | 5.50% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 1.20% | 98.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 52.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522020155 | G -> A | LOC_Os05g37620.1 | missense_variant ; p.Ser233Leu; MODERATE | nonsynonymous_codon ; S233L | Average:14.139; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
0.42 |
TOLERATED | 0.15 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0522020155 | 7.74E-07 | NA | mr1707 | 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 |
| vg0522020155 | 8.38E-06 | 7.68E-06 | mr1707 | 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 |
| vg0522020155 | 2.26E-06 | NA | mr1728 | 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 |
| vg0522020155 | 7.19E-06 | 5.21E-06 | mr1728 | 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 |