Search for Variation information by Variation ID:
Detailed information for vg0817401463:
| Variant ID: vg0817401463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17401463 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
TTTAGTTGAACCACCTTCTGGACATAATATTATTGGAACCAAGTGGGTTTTCAAAAATAAACAAAATGAGGATGGTTTGATTGTGAGAAATAAAGCTAGA[C/T]
TTGTTGCTCAAGATTTTACCCAGGTTGAGGGTTTGGATTTTGTTGAAACTTTTGCTCCTGTTGCTAGAATTGAGGCAATTAGACTTTTGTTGGCTTTTCC
Reverse complement sequence
GGAAAAGCCAACAAAAGTCTAATTGCCTCAATTCTAGCAACAGGAGCAAAAGTTTCAACAAAATCCAAACCCTCAACCTGGGTAAAATCTTGAGCAACAA[G/A]
TCTAGCTTTATTTCTCACAATCAAACCATCCTCATTTTGTTTATTTTTGAAAACCCACTTGGTTCCAATAATATTATGTCCAGAAGGTGGTTCAACTAAA
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 | 52.90% | 1.60% | 2.09% | 43.46% | NA |
| All Indica | 2759 | 25.60% | 0.40% | 2.25% | 71.73% | NA |
| All Japonica | 1512 | 91.30% | 4.10% | 2.25% | 2.38% | NA |
| Aus | 269 | 94.80% | 0.00% | 0.37% | 4.83% | NA |
| Indica I | 595 | 38.50% | 1.20% | 1.85% | 58.49% | NA |
| Indica II | 465 | 16.80% | 0.20% | 2.15% | 80.86% | NA |
| Indica III | 913 | 22.20% | 0.00% | 2.41% | 75.36% | NA |
| Indica Intermediate | 786 | 24.90% | 0.50% | 2.42% | 72.14% | NA |
| Temperate Japonica | 767 | 89.00% | 6.60% | 3.65% | 0.65% | NA |
| Tropical Japonica | 504 | 93.80% | 0.00% | 0.40% | 5.75% | NA |
| Japonica Intermediate | 241 | 92.90% | 4.60% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 68.90% | 1.10% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0817401463 | C -> T | LOC_Os08g28500.1 | missense_variant ; p.Leu608Phe; MODERATE | nonsynonymous_codon ; L608F | Average:11.565; most accessible tissue: Zhenshan97 flag leaf, score: 20.297 | benign  |
1.197 |
DELETERIOUS | 0.02 |
| vg0817401463 | C -> DEL | LOC_Os08g28500.1 | N | frameshift_variant | Average:11.565; most accessible tissue: Zhenshan97 flag leaf, score: 20.297 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817401463 | NA | 8.49E-06 | mr1126 | 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 |
| vg0817401463 | 1.19E-06 | 1.19E-06 | mr1687 | 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 |