Search for Variation information by Variation ID:
Detailed information for vg0207793492:
| Variant ID: vg0207793492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 7793492 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCATATACAACCGCGTGGGCTGGAATGCACGGAATGGTGTTACGGACCTGACAAAAGCGTTGTATGTACGAACGGAGGGATTCATCATCCTTCTGCCGCA[C/T]
AGCATGCAGGTCCGCCTCTTCCCCTGGGCGAGGATATGTGCCTTGGAAGTTTGTGATGAACTGCTGGGACAAGTCCTCCCAGGAGTGAATGGAGTCGGGG
Reverse complement sequence
CCCCGACTCCATTCACTCCTGGGAGGACTTGTCCCAGCAGTTCATCACAAACTTCCAAGGCACATATCCTCGCCCAGGGGAAGAGGCGGACCTGCATGCT[G/A]
TGCGGCAGAAGGATGATGAATCCCTCCGTTCGTACATACAACGCTTTTGTCAGGTCCGTAACACCATTCCGTGCATTCCAGCCCACGCGGTTGTATATGC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.80% | 12.30% | 0.87% | 50.13% | NA |
| All Indica | 2759 | 6.90% | 8.50% | 1.49% | 83.18% | NA |
| All Japonica | 1512 | 97.20% | 0.30% | 0.00% | 2.45% | NA |
| Aus | 269 | 0.40% | 99.30% | 0.00% | 0.37% | NA |
| Indica I | 595 | 2.70% | 0.30% | 1.51% | 95.46% | NA |
| Indica II | 465 | 5.20% | 2.20% | 2.15% | 90.54% | NA |
| Indica III | 913 | 9.70% | 16.20% | 0.77% | 73.27% | NA |
| Indica Intermediate | 786 | 7.60% | 9.40% | 1.91% | 81.04% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 95.80% | 0.20% | 0.00% | 3.97% | NA |
| Japonica Intermediate | 241 | 96.70% | 1.70% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 39.60% | 60.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 16.70% | 0.00% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0207793492 | C -> T | LOC_Os02g14220.1 | missense_variant ; p.Val337Met; MODERATE | nonsynonymous_codon ; V337M | Average:11.029; most accessible tissue: Callus, score: 42.823 | benign  |
1.231 |
DELETERIOUS | 0.00 |
| vg0207793492 | C -> DEL | LOC_Os02g14220.1 | N | frameshift_variant | Average:11.029; most accessible tissue: Callus, score: 42.823 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0207793492 | NA | 3.67E-10 | mr1522_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 |