Search for Variation information by Variation ID:
Detailed information for vg1013475468:
| Variant ID: vg1013475468 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 13475468 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
CCGTTCCCAGGAATGGCAAACTATCGAGCAGAGGCGCCGCTCGAGCTGCTCCACATGGATCTGTGTGGGCCGATCACTCCATCGACGTTCGCCGGTAATC[G/A]
ATACTTTATGTTGATCGTTGATGATTTTTCTAATTGGATGTGGGTGTTTGTGATCAAGTTGAAGGACCAAGCGCTCGCGGTGTTCGAGAAGTTCAAGCCG
Reverse complement sequence
CGGCTTGAACTTCTCGAACACCGCGAGCGCTTGGTCCTTCAACTTGATCACAAACACCCACATCCAATTAGAAAAATCATCAACGATCAACATAAAGTAT[C/T]
GATTACCGGCGAACGTCGATGGAGTGATCGGCCCACACAGATCCATGTGGAGCAGCTCGAGCGGCGCCTCTGCTCGATAGTTTGCCATTCCTGGGAACGG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 8.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 74.20% | 25.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 51.20% | 48.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1013475468 | G -> A | LOC_Os10g26030.1 | missense_variant ; p.Arg421Gln; MODERATE | nonsynonymous_codon ; R421Q | Average:50.444; most accessible tissue: Minghui63 young leaf, score: 66.656 | benign  |
1.049 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013475468 | 1.44E-06 | NA | mr1533 | 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 |
| vg1013475468 | 7.51E-07 | 8.81E-15 | mr1533 | Jap_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 |
| vg1013475468 | 4.41E-07 | NA | mr1980 | 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 |
| vg1013475468 | 2.56E-09 | 6.67E-22 | mr1980 | Jap_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 |
| vg1013475468 | 2.78E-06 | NA | mr1533_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 |
| vg1013475468 | 2.51E-10 | 2.27E-24 | mr1533_2 | Jap_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 |
| vg1013475468 | 9.33E-06 | 1.84E-10 | mr1980_2 | Jap_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 |