Search for Variation information by Variation ID:
Detailed information for vg0712942751:
| Variant ID: vg0712942751 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12942751 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
CAAATCTCTATCAGTTATATTCAAAGTATAACATCGGTTTCTAACATCCCTAAATCTCTTAATATAATCAATGACAGATTCATTGTATTTTTGCTTAACC[G/A]
ATGTCAAATCACATAACCTAAGCTCAGTTTCTCCAGTATAGAAATAATCATGAAATTTTTCTTCTAATTGAGCCCAAGTATGAATAGATTTTGCCGGTAA
Reverse complement sequence
TTACCGGCAAAATCTATTCATACTTGGGCTCAATTAGAAGAAAAATTTCATGATTATTTCTATACTGGAGAAACTGAGCTTAGGTTATGTGATTTGACAT[C/T]
GGTTAAGCAAAAATACAATGAATCTGTCATTGATTATATTAAGAGATTTAGGGATGTTAGAAACCGATGTTATACTTTGAATATAACTGATAGAGATTTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.90% | 4.40% | 25.41% | 4.27% | NA |
| All Indica | 2759 | 49.50% | 7.20% | 37.48% | 5.80% | NA |
| All Japonica | 1512 | 89.60% | 0.50% | 7.61% | 2.31% | NA |
| Aus | 269 | 88.50% | 0.00% | 10.78% | 0.74% | NA |
| Indica I | 595 | 31.60% | 14.50% | 50.08% | 3.87% | NA |
| Indica II | 465 | 51.60% | 4.30% | 36.77% | 7.31% | NA |
| Indica III | 913 | 61.60% | 3.50% | 28.81% | 6.13% | NA |
| Indica Intermediate | 786 | 48.00% | 7.60% | 38.42% | 5.98% | NA |
| Temperate Japonica | 767 | 86.40% | 0.90% | 8.47% | 4.17% | NA |
| Tropical Japonica | 504 | 92.30% | 0.00% | 7.34% | 0.40% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.40% | 5.39% | 0.41% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 12.50% | 2.08% | NA |
| Intermediate | 90 | 81.10% | 3.30% | 12.22% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712942751 | G -> DEL | LOC_Os07g22960.1 | N | frameshift_variant | Average:5.34; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |
| vg0712942751 | G -> A | LOC_Os07g22960.1 | missense_variant ; p.Ser668Leu; MODERATE | nonsynonymous_codon ; S668L | Average:5.34; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | benign  |
0.119 |
TOLERATED | 0.08 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712942751 | 5.35E-07 | 2.53E-07 | mr1917 | 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 |
| vg0712942751 | NA | 1.55E-06 | mr1936 | 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 |