Search for Variation information by Variation ID:
Detailed information for vg1208562683:
| Variant ID: vg1208562683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8562683 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTCTCGCAATTTCTCCCAGTCACCGTTTACATACCCGACGGTAGATGTGCACCATTGTTTCGCTCTCTCATGAAGAGAGAACGGAAACAATTTCCACC[G/A]
AACAGTCTCTTGCTTCATGCCTCGAATCTTAAGGCACGAGCAAAGCTGCTCAAATTCCCGCAGATGATGGTAGGGGTTTTCCTGGCCTAAACTAGAGAAA
Reverse complement sequence
TTTCTCTAGTTTAGGCCAGGAAAACCCCTACCATCATCTGCGGGAATTTGAGCAGCTTTGCTCGTGCCTTAAGATTCGAGGCATGAAGCAAGAGACTGTT[C/T]
GGTGGAAATTGTTTCCGTTCTCTCTTCATGAGAGAGCGAAACAATGGTGCACATCTACCGTCGGGTATGTAAACGGTGACTGGGAGAAATTGCGAGACAG
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 | 87.20% | 3.40% | 5.08% | 4.32% | NA |
| All Indica | 2759 | 80.30% | 5.30% | 8.19% | 6.16% | NA |
| All Japonica | 1512 | 97.40% | 0.10% | 0.46% | 2.05% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.00% | 1.80% | 1.34% | 0.84% | NA |
| Indica II | 465 | 79.80% | 4.70% | 7.53% | 7.96% | NA |
| Indica III | 913 | 66.30% | 8.50% | 14.57% | 10.62% | NA |
| Indica Intermediate | 786 | 85.10% | 4.60% | 6.36% | 3.94% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.39% | 3.39% | NA |
| Tropical Japonica | 504 | 98.40% | 0.00% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 6.20% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 2.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208562683 | G -> DEL | LOC_Os12g14960.1 | N | frameshift_variant | Average:10.701; most accessible tissue: Callus, score: 24.394 | N | N | N | N |
| vg1208562683 | G -> A | LOC_Os12g14960.1 | missense_variant ; p.Arg79Trp; MODERATE | nonsynonymous_codon ; R79W | Average:10.701; most accessible tissue: Callus, score: 24.394 | benign  |
0.514 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208562683 | 4.78E-06 | 2.88E-06 | mr1042_2 | Ind_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 |
| vg1208562683 | 1.06E-08 | 3.48E-09 | mr1871_2 | Ind_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 |