Search for Variation information by Variation ID:
Detailed information for vg0717479191:
| Variant ID: vg0717479191 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 17479191 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGCCAATGATGTAACGCAAGTCTTTTACGTGAAGGACATGTCTAGCATAGGAAAGAAGGGCAGAGGACCTGACGAGCCGAAGCGTCACGTGGTTCTCC[C/T]
AGGCAAAAGAAAAATCGTCGGAGTTGAGGACAAGACTGACGAGGATTACGATTAGTTGGATGGGCAACCCCCTTTCACGGTGACGATTGACCCTAGCATC
Reverse complement sequence
GATGCTAGGGTCAATCGTCACCGTGAAAGGGGGTTGCCCATCCAACTAATCGTAATCCTCGTCAGTCTTGTCCTCAACTCCGACGATTTTTCTTTTGCCT[G/A]
GGAGAACCACGTGACGCTTCGGCTCGTCAGGTCCTCTGCCCTTCTTTCCTATGCTAGACATGTCCTTCACGTAAAAGACTTGCGTTACATCATTGGCAAG
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 | 91.10% | 2.10% | 4.74% | 2.14% | NA |
| All Indica | 2759 | 90.70% | 0.10% | 5.65% | 3.52% | NA |
| All Japonica | 1512 | 90.00% | 6.20% | 3.84% | 0.00% | NA |
| Aus | 269 | 97.00% | 0.00% | 2.23% | 0.74% | NA |
| Indica I | 595 | 84.00% | 0.20% | 14.29% | 1.51% | NA |
| Indica II | 465 | 93.30% | 0.00% | 3.66% | 3.01% | NA |
| Indica III | 913 | 95.20% | 0.10% | 1.20% | 3.50% | NA |
| Indica Intermediate | 786 | 89.10% | 0.10% | 5.47% | 5.34% | NA |
| Temperate Japonica | 767 | 83.40% | 10.40% | 6.13% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 1.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 3.30% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 4.44% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0717479191 | C -> DEL | LOC_Os07g29730.1 | N | frameshift_variant | Average:13.834; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0717479191 | C -> T | LOC_Os07g29730.1 | missense_variant ; p.Pro809Leu; MODERATE | nonsynonymous_codon ; P809L | Average:13.834; most accessible tissue: Zhenshan97 panicle, score: 20.424 | probably damaging  |
2.029 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0717479191 | NA | 3.47E-07 | mr1567_2 | 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 |
| vg0717479191 | NA | 6.69E-08 | mr1588_2 | 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 |
| vg0717479191 | 1.03E-06 | 1.03E-06 | mr1806_2 | 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 |