Search for Variation information by Variation ID:
Detailed information for vg0427224260:
| Variant ID: vg0427224260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 27224260 |
| 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, A: 0.00, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
TTCGTTCAGCCCATGGATAACAAGTGTTGGGGCATCCACAACTGACAGGAAGTATAACAAATCAATTATAATTGGAAATGGGCAAGTCTTCTCTTGCGGC[G/A]
GCCTATCACGTAATTCATTTCAACCTATGAAATTAATGAATTTGGAGCCTTCTCAAGTTCTAGTGTTTAACTGATGATACTAAGTTCCATACTTCTCTTT
Reverse complement sequence
AAAGAGAAGTATGGAACTTAGTATCATCAGTTAAACACTAGAACTTGAGAAGGCTCCAAATTCATTAATTTCATAGGTTGAAATGAATTACGTGATAGGC[C/T]
GCCGCAAGAGAAGACTTGCCCATTTCCAATTATAATTGATTTGTTATACTTCCTGTCAGTTGTGGATGCCCCAACACTTGTTATCCATGGGCTGAACGAA
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 | 95.70% | 4.10% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 86.90% | 12.60% | 0.53% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.60% | 3.10% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 73.20% | 25.80% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 84.60% | 14.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0427224260 | G -> A | LOC_Os04g45960.1 | missense_variant ; p.Gly406Ser; MODERATE | nonsynonymous_codon ; G406S | Average:52.464; most accessible tissue: Callus, score: 91.326 | benign  |
1.453 |
TOLERATED | 0.11 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0427224260 | NA | 3.78E-15 | mr1769 | 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 |
| vg0427224260 | NA | 4.92E-14 | mr1951 | Jap_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 |
| vg0427224260 | NA | 2.68E-08 | mr1676_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 |
| vg0427224260 | 5.07E-06 | 5.25E-20 | mr1769_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 |
| vg0427224260 | NA | 5.98E-07 | mr1951_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 |