Search for Variation information by Variation ID:
Detailed information for vg0714470500:
| Variant ID: vg0714470500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14470500 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCACACCCCTGGCTTGCTTCCCTGTTCCTTCCTAACGGGCTGGTTCTGAGCTGGAGTTGCTGCAGGACGAGCGACCATATTGCGGTTGTCATTGGTGCG[G/A]
TTACCAGTATTGTTGTGGTAGAACTGGCGTTGAGGGCGGACAACTAATGAAGATCCTCCTTGAGGGTACGATGGAGCTTGAGGTCCCGTAACGAGACGCG
Reverse complement sequence
CGCGTCTCGTTACGGGACCTCAAGCTCCATCGTACCCTCAAGGAGGATCTTCATTAGTTGTCCGCCCTCAACGCCAGTTCTACCACAACAATACTGGTAA[C/T]
CGCACCAATGACAACCGCAATATGGTCGCTCGTCCTGCAGCAACTCCAGCTCAGAACCAGCCCGTTAGGAAGGAACAGGGAAGCAAGCCAGGGGTGTGCT
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 | 78.40% | 1.30% | 8.38% | 11.96% | NA |
| All Indica | 2759 | 73.00% | 0.50% | 10.76% | 15.80% | NA |
| All Japonica | 1512 | 88.00% | 1.90% | 3.97% | 6.15% | NA |
| Aus | 269 | 70.30% | 7.10% | 13.01% | 9.67% | NA |
| Indica I | 595 | 73.60% | 0.00% | 6.39% | 20.00% | NA |
| Indica II | 465 | 72.90% | 0.00% | 9.68% | 17.42% | NA |
| Indica III | 913 | 70.30% | 0.70% | 14.02% | 15.01% | NA |
| Indica Intermediate | 786 | 75.60% | 0.90% | 10.94% | 12.60% | NA |
| Temperate Japonica | 767 | 86.30% | 2.90% | 5.08% | 5.74% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 0.60% | 3.17% | NA |
| Japonica Intermediate | 241 | 75.90% | 2.90% | 7.47% | 13.69% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 4.44% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714470500 | G -> DEL | LOC_Os07g25330.1 | N | frameshift_variant | Average:24.529; most accessible tissue: Callus, score: 54.938 | N | N | N | N |
| vg0714470500 | G -> A | LOC_Os07g25330.1 | synonymous_variant ; p.Asn78Asn; LOW | synonymous_codon | Average:24.529; most accessible tissue: Callus, score: 54.938 | N | N | N | N |
| vg0714470500 | G -> A | LOC_Os07g25330.1 | synonymous_variant ; p.Asn78Asn; LOW | nonsynonymous_codon | Average:24.529; most accessible tissue: Callus, score: 54.938 | benign  |
1.099 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714470500 | 3.13E-06 | NA | mr1246_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 |