Search for Variation information by Variation ID:
Detailed information for vg0716085423:
| Variant ID: vg0716085423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16085423 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTGTCGATCGATGCGCCCACGCGGACGACGTACTGAGACGCAAGAACGACAAGCCGAAGACCGGAGGAGAGAAGAAACCAGCGAAGGACGCACCTGAGT[C/T]
AAGCAAAAAGAAAAATTGTAAGAGTGGGAAAAGGAAAGCTCAAGCGTAAGTTCTCGCAGCAGAATACGCCGACCCTGCCAAACGCCCAGACCCACAAGGT
Reverse complement sequence
ACCTTGTGGGTCTGGGCGTTTGGCAGGGTCGGCGTATTCTGCTGCGAGAACTTACGCTTGAGCTTTCCTTTTCCCACTCTTACAATTTTTCTTTTTGCTT[G/A]
ACTCAGGTGCGTCCTTCGCTGGTTTCTTCTCTCCTCCGGTCTTCGGCTTGTCGTTCTTGCGTCTCAGTACGTCGTCCGCGTGGGCGCATCGATCGACAAT
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 | 59.00% | 4.70% | 1.48% | 34.91% | NA |
| All Indica | 2759 | 42.90% | 1.60% | 1.92% | 53.57% | NA |
| All Japonica | 1512 | 88.10% | 11.40% | 0.00% | 0.46% | NA |
| Aus | 269 | 41.60% | 0.00% | 5.95% | 52.42% | NA |
| Indica I | 595 | 56.50% | 0.80% | 2.02% | 40.67% | NA |
| Indica II | 465 | 23.70% | 0.90% | 1.51% | 73.98% | NA |
| Indica III | 913 | 36.80% | 0.20% | 2.19% | 60.79% | NA |
| Indica Intermediate | 786 | 51.00% | 4.30% | 1.78% | 42.88% | NA |
| Temperate Japonica | 767 | 78.20% | 21.30% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 1.20% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 2.20% | 1.11% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0716085423 | C -> DEL | LOC_Os07g27520.1 | N | frameshift_variant | Average:11.878; most accessible tissue: Callus, score: 27.094 | N | N | N | N |
| vg0716085423 | C -> T | LOC_Os07g27520.1 | missense_variant ; p.Ser456Leu; MODERATE | nonsynonymous_codon ; S456L | Average:11.878; most accessible tissue: Callus, score: 27.094 | possibly damaging  |
1.563 |
TOLERATED | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716085423 | NA | 1.64E-06 | mr1528 | 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 |
| vg0716085423 | 3.60E-15 | 3.86E-14 | mr1265_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 |
| vg0716085423 | 6.80E-13 | 4.13E-14 | mr1528_2 | 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 |