Search for Variation information by Variation ID:
Detailed information for vg0114842613:
| Variant ID: vg0114842613 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14842613 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTCATCCTCAAGGAAATCCCGGGCTTTTCCGACCCTCATATTCTTTTTTCAGTTCAGCTATCTCAGGATCATTTACTTGAGTTGCTCTGACTTGATCCA[C/T]
GAGCGTAGGCCGTGCCTCTAGAGCAGCCACAAACCCGTGTTCTACGATTCCCAAGTTGAGATGTTCAAGCTCCTGCTGCAATTCCTTACACATGCCTTCG
Reverse complement sequence
CGAAGGCATGTGTAAGGAATTGCAGCAGGAGCTTGAACATCTCAACTTGGGAATCGTAGAACACGGGTTTGTGGCTGCTCTAGAGGCACGGCCTACGCTC[G/A]
TGGATCAAGTCAGAGCAACTCAAGTAAATGATCCTGAGATAGCTGAACTGAAAAAAGAATATGAGGGTCGGAAAAGCCCGGGATTTCCTTGAGGATGAAC
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 | 50.80% | 1.70% | 12.67% | 34.85% | NA |
| All Indica | 2759 | 33.20% | 0.10% | 18.88% | 47.88% | NA |
| All Japonica | 1512 | 79.80% | 4.60% | 3.51% | 12.04% | NA |
| Aus | 269 | 69.50% | 0.00% | 4.83% | 25.65% | NA |
| Indica I | 595 | 53.30% | 0.00% | 9.58% | 37.14% | NA |
| Indica II | 465 | 41.10% | 0.20% | 13.33% | 45.38% | NA |
| Indica III | 913 | 13.00% | 0.00% | 28.70% | 58.27% | NA |
| Indica Intermediate | 786 | 36.60% | 0.10% | 17.81% | 45.42% | NA |
| Temperate Japonica | 767 | 81.50% | 8.90% | 4.30% | 5.35% | NA |
| Tropical Japonica | 504 | 90.10% | 0.00% | 2.58% | 7.34% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.80% | 2.90% | 43.15% | NA |
| VI/Aromatic | 96 | 40.60% | 0.00% | 7.29% | 52.08% | NA |
| Intermediate | 90 | 57.80% | 8.90% | 5.56% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114842613 | C -> T | LOC_Os01g26190.1 | missense_variant ; p.Val536Met; MODERATE | nonsynonymous_codon ; V536M | Average:8.343; most accessible tissue: Callus, score: 17.882 | probably damaging  |
2.247 |
DELETERIOUS | 0.03 |
| vg0114842613 | C -> DEL | LOC_Os01g26190.1 | N | frameshift_variant | Average:8.343; most accessible tissue: Callus, score: 17.882 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114842613 | NA | 2.45E-06 | mr1330_2 | 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 |