Search for Variation information by Variation ID:
Detailed information for vg1116692722:
| Variant ID: vg1116692722 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16692722 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTTCATGTTGAGGATGGCATTGAGTTTCTCCGGGTTGGCTTGTATGCCTCTATGGGACACCATGAATCCAAGCAGCTTCCCTGACGGTACTCCGAAGATG[C/A]
ATTTTTCAGGGTTTAGTTTCATCCTGAAAGCGCGGATGCTTGCAAAGGTCTCTTCTAGATCCGTAATCAGATCATCCTTCTGCTTGGTCTTAACGACTAC
Reverse complement sequence
GTAGTCGTTAAGACCAAGCAGAAGGATGATCTGATTACGGATCTAGAAGAGACCTTTGCAAGCATCCGCGCTTTCAGGATGAAACTAAACCCTGAAAAAT[G/T]
CATCTTCGGAGTACCGTCAGGGAAGCTGCTTGGATTCATGGTGTCCCATAGAGGCATACAAGCCAACCCGGAGAAACTCAATGCCATCCTCAACATGAAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.40% | 0.70% | 4.95% | 17.92% | NA |
| All Indica | 2759 | 64.20% | 1.10% | 6.85% | 27.91% | NA |
| All Japonica | 1512 | 95.90% | 0.10% | 0.26% | 3.77% | NA |
| Aus | 269 | 82.50% | 1.10% | 13.01% | 3.35% | NA |
| Indica I | 595 | 80.50% | 0.70% | 1.85% | 16.97% | NA |
| Indica II | 465 | 55.30% | 0.90% | 9.46% | 34.41% | NA |
| Indica III | 913 | 58.40% | 1.30% | 7.89% | 32.42% | NA |
| Indica Intermediate | 786 | 63.70% | 1.30% | 7.89% | 27.10% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.13% | 1.96% | NA |
| Tropical Japonica | 504 | 92.50% | 0.20% | 0.40% | 6.94% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 1.10% | 6.67% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116692722 | C -> A | LOC_Os11g28810.1 | missense_variant ; p.Cys282Phe; MODERATE | nonsynonymous_codon ; C282F | Average:29.467; most accessible tissue: Zhenshan97 panicle, score: 49.416 | probably damaging  |
2.413 |
DELETERIOUS | 0.01 |
| vg1116692722 | C -> DEL | LOC_Os11g28810.1 | N | frameshift_variant | Average:29.467; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116692722 | 3.48E-06 | NA | mr1237 | 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 |