Search for Variation information by Variation ID:
Detailed information for vg0716356793:
| Variant ID: vg0716356793 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16356793 |
| 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: 250. )
Flanking Sequence (100 bp) in Reference Genome:
CGATTCGGTCCACCTCTTTTCCTGTTCCTAACATTATTCATAGCTCGAGAAAATTTGTTAGATAGCAAAACCAAGTCCTCCTCGAACTGTTCAAGTTGAT[C/T]
GTCGAACATGGCATTAAATAAAGCAAGAACAGAAGACTTCGATGAAGAAGCATCAACATCCAAAGAAGTTGTAGACGAAACCAAAGCACTATACTTAGAA
Reverse complement sequence
TTCTAAGTATAGTGCTTTGGTTTCGTCTACAACTTCTTTGGATGTTGATGCTTCTTCATCGAAGTCTTCTGTTCTTGCTTTATTTAATGCCATGTTCGAC[G/A]
ATCAACTTGAACAGTTCGAGGAGGACTTGGTTTTGCTATCTAACAAATTTTCTCGAGCTATGAATAATGTTAGGAACAGGAAAAGAGGTGGACCGAATCG
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 | 85.00% | 15.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 88.90% | 11.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 31.60% | 68.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 76.50% | 23.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0716356793 | C -> T | LOC_Os07g28050.1 | missense_variant ; p.Asp571Asn; MODERATE | nonsynonymous_codon ; D571N | Average:26.953; most accessible tissue: Minghui63 young leaf, score: 51.901 | possibly damaging  |
1.653 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716356793 | NA | 9.64E-07 | mr1697 | 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 |
| vg0716356793 | NA | 7.91E-06 | mr1697 | Ind_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 |