Search for Variation information by Variation ID:
Detailed information for vg0804877336:
| Variant ID: vg0804877336 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4877336 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTTCATCTCATGAACCCCACTATAGAAATAACTGTGAAACTGCTTCTCTAAATCAGCCCAACTGTTAATCGACCCATGTGGCAGAGAAGAAAACCAAGT[A/T]
AAAGCCGACCCAGCTAATGACAACCGGAATAACCTAACCCTCAAAGCATCTACAGCCGATGCCTCACCACACTGAGCTAAGAATCGGCTGATGTGCTCAT
Reverse complement sequence
ATGAGCACATCAGCCGATTCTTAGCTCAGTGTGGTGAGGCATCGGCTGTAGATGCTTTGAGGGTTAGGTTATTCCGGTTGTCATTAGCTGGGTCGGCTTT[T/A]
ACTTGGTTTTCTTCTCTGCCACATGGGTCGATTAACAGTTGGGCTGATTTAGAGAAGCAGTTTCACAGTTATTTCTATAGTGGGGTTCATGAGATGAAGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.00% | 2.10% | 0.89% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 91.70% | 6.40% | 1.92% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 0.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 86.90% | 9.70% | 3.37% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.40% | 17.00% | 4.56% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 13.54% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804877336 | A -> T | LOC_Os08g08460.1 | missense_variant ; p.Phe502Leu; MODERATE | nonsynonymous_codon ; F502L | Average:33.408; most accessible tissue: Minghui63 flag leaf, score: 76.453 | benign  |
0.656 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804877336 | 1.31E-06 | 1.35E-07 | mr1543 | 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 |