Search for Variation information by Variation ID:
Detailed information for vg1116692719:
| Variant ID: vg1116692719 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16692719 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGTTTCATGTTGAGGATGGCATTGAGTTTCTCCGGGTTGGCTTGTATGCCTCTATGGGACACCATGAATCCAAGCAGCTTCCCTGACGGTACTCCGAAG[A/T]
TGCATTTTTCAGGGTTTAGTTTCATCCTGAAAGCGCGGATGCTTGCAAAGGTCTCTTCTAGATCCGTAATCAGATCATCCTTCTGCTTGGTCTTAACGAC
Reverse complement sequence
GTCGTTAAGACCAAGCAGAAGGATGATCTGATTACGGATCTAGAAGAGACCTTTGCAAGCATCCGCGCTTTCAGGATGAAACTAAACCCTGAAAAATGCA[T/A]
CTTCGGAGTACCGTCAGGGAAGCTGCTTGGATTCATGGTGTCCCATAGAGGCATACAAGCCAACCCGGAGAAACTCAATGCCATCCTCAACATGAAACCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.50% | 1.30% | 6.20% | 21.05% | NA |
| All Indica | 2759 | 61.50% | 0.60% | 5.18% | 32.66% | NA |
| All Japonica | 1512 | 95.90% | 0.00% | 0.00% | 4.10% | NA |
| Aus | 269 | 23.40% | 16.00% | 53.90% | 6.69% | NA |
| Indica I | 595 | 79.70% | 0.30% | 1.68% | 18.32% | NA |
| Indica II | 465 | 54.00% | 0.20% | 5.81% | 40.00% | NA |
| Indica III | 913 | 54.30% | 0.80% | 6.79% | 38.12% | NA |
| Indica Intermediate | 786 | 60.70% | 0.90% | 5.60% | 32.82% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.00% | 2.09% | NA |
| Tropical Japonica | 504 | 92.50% | 0.00% | 0.00% | 7.54% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 4.44% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116692719 | A -> T | LOC_Os11g28810.1 | missense_variant ; p.Ile283Asn; MODERATE | nonsynonymous_codon ; I283N | Average:29.522; most accessible tissue: Zhenshan97 panicle, score: 49.416 | possibly damaging  |
1.623 |
DELETERIOUS | 0.00 |
| vg1116692719 | A -> DEL | LOC_Os11g28810.1 | N | frameshift_variant | Average:29.522; 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 |
|---|---|---|---|---|---|---|
| vg1116692719 | 9.72E-06 | NA | mr1091 | Ind_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 |
| vg1116692719 | 3.68E-06 | NA | mr1112 | 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 |
| vg1116692719 | NA | 1.67E-07 | mr1004_2 | 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 |