Search for Variation information by Variation ID:
Detailed information for vg0218158093:
| Variant ID: vg0218158093 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 18158093 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAACGGAATATGGCGTGGCGGCAATATAAAGGAATAATTTTTCATTAGGTTGGGGAGCAACGAGTACAGGGGGGTTTGATAGGTAGCGCTTGAGTGCAAT[A/T]
AATGCCTCTTTGGCTTCCTGTGTCCATACAAAGTTGTCTTGTTTCTTCAACAAGGCGAAGAAAGGCTGTCTTCGTTCTCCCATCCTAGCGACGAATCTGC
Reverse complement sequence
GCAGATTCGTCGCTAGGATGGGAGAACGAAGACAGCCTTTCTTCGCCTTGTTGAAGAAACAAGACAACTTTGTATGGACACAGGAAGCCAAAGAGGCATT[T/A]
ATTGCACTCAAGCGCTACCTATCAAACCCCCCTGTACTCGTTGCTCCCCAACCTAATGAAAAATTATTCCTTTATATTGCCGCCACGCCATATTCCGTTA
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 | 67.20% | 4.40% | 11.68% | 16.65% | NA |
| All Indica | 2759 | 72.10% | 4.50% | 14.57% | 8.77% | NA |
| All Japonica | 1512 | 63.60% | 0.00% | 1.52% | 34.92% | NA |
| Aus | 269 | 25.70% | 30.50% | 42.38% | 1.49% | NA |
| Indica I | 595 | 79.20% | 1.70% | 10.25% | 8.91% | NA |
| Indica II | 465 | 89.20% | 1.10% | 6.24% | 3.44% | NA |
| Indica III | 913 | 57.60% | 7.60% | 23.11% | 11.72% | NA |
| Indica Intermediate | 786 | 73.50% | 5.20% | 12.85% | 8.40% | NA |
| Temperate Japonica | 767 | 95.30% | 0.00% | 0.39% | 4.30% | NA |
| Tropical Japonica | 504 | 13.70% | 0.00% | 2.38% | 83.93% | NA |
| Japonica Intermediate | 241 | 66.80% | 0.00% | 3.32% | 29.88% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 1.10% | 12.22% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0218158093 | A -> T | LOC_Os02g30510.1 | missense_variant ; p.Phe233Leu; MODERATE | nonsynonymous_codon ; F233L | Average:13.982; most accessible tissue: Callus, score: 23.728 | possibly damaging  |
1.576 |
TOLERATED | 0.32 |
| vg0218158093 | A -> DEL | LOC_Os02g30510.1 | N | frameshift_variant | Average:13.982; most accessible tissue: Callus, score: 23.728 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0218158093 | NA | 3.57E-06 | mr1206_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 |
| vg0218158093 | 5.96E-06 | 3.17E-06 | mr1209_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 |
| vg0218158093 | 1.69E-06 | 8.92E-06 | mr1415_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 |
| vg0218158093 | NA | 4.84E-06 | mr1603_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 |
| vg0218158093 | 5.70E-06 | 5.70E-06 | mr1787_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 |