Search for Variation information by Variation ID:
Detailed information for vg1217046463:
| Variant ID: vg1217046463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17046463 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCGGCTGATGAGGTGCCCGTCAAGGAGATCCCCCTTGGCGATGATGTGTCCAAGACCGCCAAAATTGGCGGAAACCTGGGCGCCAAATAGGAAGGCGCG[C/T]
TTGTCTCCTTCCTTCGGGCAAATTCTGACGTCTTCGCATGGAAGCTGTCAGATATGCCCAGGGTCCTCAAGGAGGTGATCGAGCACCGCTTTGCCGTCCG
Reverse complement sequence
CGGACGGCAAAGCGGTGCTCGATCACCTCCTTGAGGACCCTGGGCATATCTGACAGCTTCCATGCGAAGACGTCAGAATTTGCCCGAAGGAAGGAGACAA[G/A]
CGCGCCTTCCTATTTGGCGCCCAGGTTTCCGCCAATTTTGGCGGTCTTGGACACATCATCGCCAAGGGGGATCTCCTTGACGGGCACCTCATCAGCCGAG
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 | 82.30% | 1.10% | 3.43% | 13.18% | NA |
| All Indica | 2759 | 86.70% | 0.00% | 1.70% | 11.56% | NA |
| All Japonica | 1512 | 86.20% | 3.30% | 4.17% | 6.28% | NA |
| Aus | 269 | 24.90% | 0.00% | 16.36% | 58.74% | NA |
| Indica I | 595 | 96.00% | 0.00% | 0.00% | 4.03% | NA |
| Indica II | 465 | 83.20% | 0.00% | 2.80% | 13.98% | NA |
| Indica III | 913 | 84.60% | 0.00% | 1.97% | 13.47% | NA |
| Indica Intermediate | 786 | 84.40% | 0.00% | 2.04% | 13.61% | NA |
| Temperate Japonica | 767 | 91.90% | 0.90% | 5.08% | 2.09% | NA |
| Tropical Japonica | 504 | 86.30% | 2.80% | 0.79% | 10.12% | NA |
| Japonica Intermediate | 241 | 68.00% | 12.00% | 8.30% | 11.62% | NA |
| VI/Aromatic | 96 | 49.00% | 0.00% | 7.29% | 43.75% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 1.11% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217046463 | C -> DEL | LOC_Os12g28830.1 | N | frameshift_variant | Average:65.22; most accessible tissue: Zhenshan97 young leaf, score: 86.22 | N | N | N | N |
| vg1217046463 | C -> T | LOC_Os12g28830.1 | missense_variant ; p.Leu492Phe; MODERATE | nonsynonymous_codon ; L492F | Average:65.22; most accessible tissue: Zhenshan97 young leaf, score: 86.22 | possibly damaging  |
1.952 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217046463 | NA | 1.27E-06 | mr1691 | 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 |
| vg1217046463 | 3.57E-08 | 1.91E-12 | mr1693 | 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 |