Search for Variation information by Variation ID:
Detailed information for vg0807428848:
| Variant ID: vg0807428848 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7428848 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAACTTGTTAGAGTCGAACTGCTTGCCGTTGTCAGTGATGAACTCTTTTGGCACTCCGAAACGGCAAATAATGTTTTTCCATACAAACTTCTGTACTGCT[G/A]
CCGAAGTGAATGCTCCGAGGGGTTCGGCCTCAATCCATCGGGAGAAGTATTCGATGGCCACAATTGCGAACTTGTAGCGATTTCGTGCCACTGGGAACAG
Reverse complement sequence
CTGTTCCCAGTGGCACGAAATCGCTACAAGTTCGCAATTGTGGCCATCGAATACTTCTCCCGATGGATTGAGGCCGAACCCCTCGGAGCATTCACTTCGG[C/T]
AGCAGTACAGAAGTTTGTATGGAAAAACATTATTTGCCGTTTCGGAGTGCCAAAAGAGTTCATCACTGACAACGGCAAGCAGTTCGACTCTAACAAGTTC
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 | 89.20% | 9.90% | 0.87% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.50% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 69.10% | 29.00% | 1.85% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.34% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.50% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 87.50% | 9.90% | 2.61% | 0.00% | NA |
| Tropical Japonica | 504 | 34.30% | 64.50% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 83.40% | 15.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 18.90% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0807428848 | G -> A | LOC_Os08g12550.1 | missense_variant ; p.Ala278Val; MODERATE | nonsynonymous_codon ; A278V | Average:46.915; most accessible tissue: Minghui63 young leaf, score: 80.883 | possibly damaging  |
1.768 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0807428848 | 4.60E-07 | NA | mr1588_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 |