Search for Variation information by Variation ID:
Detailed information for vg0224317158:
| Variant ID: vg0224317158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24317158 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTACACGGCTGACAGAGCTCTATCTGGAAAAAAATGCATTTGAAGGTCACATACCACCCTCCTTGGGAAACCCTCCACTACTCTTAAAGCTGGATCTT[A/G]
CCTACAACAATCTTCAAGGCACCATACCTTGGGAGATTAGTAATCTTAGACAACTCGTCTACCTGAAACTTACATCAAACAAGCTTACTGGGAATATACC
Reverse complement sequence
GGTATATTCCCAGTAAGCTTGTTTGATGTAAGTTTCAGGTAGACGAGTTGTCTAAGATTACTAATCTCCCAAGGTATGGTGCCTTGAAGATTGTTGTAGG[T/C]
AAGATCCAGCTTTAAGAGTAGTGGAGGGTTTCCCAAGGAGGGTGGTATGTGACCTTCAAATGCATTTTTTTCCAGATAGAGCTCTGTCAGCCGTGTAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.40% | 1.10% | 1.74% | 22.79% | NA |
| All Indica | 2759 | 79.00% | 0.60% | 1.05% | 19.35% | NA |
| All Japonica | 1512 | 65.10% | 1.90% | 2.65% | 30.29% | NA |
| Aus | 269 | 85.50% | 0.40% | 2.60% | 11.52% | NA |
| Indica I | 595 | 93.40% | 0.00% | 0.50% | 6.05% | NA |
| Indica II | 465 | 83.70% | 0.20% | 1.08% | 15.05% | NA |
| Indica III | 913 | 69.30% | 0.90% | 1.31% | 28.48% | NA |
| Indica Intermediate | 786 | 76.50% | 1.00% | 1.15% | 21.37% | NA |
| Temperate Japonica | 767 | 65.80% | 0.50% | 1.69% | 31.94% | NA |
| Tropical Japonica | 504 | 63.30% | 2.80% | 3.37% | 30.56% | NA |
| Japonica Intermediate | 241 | 66.80% | 4.60% | 4.15% | 24.48% | NA |
| VI/Aromatic | 96 | 52.10% | 1.00% | 4.17% | 42.71% | NA |
| Intermediate | 90 | 80.00% | 3.30% | 2.22% | 14.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224317158 | A -> G | LOC_Os02g40180.1 | missense_variant ; p.Thr467Ala; MODERATE | nonsynonymous_codon ; T467A | Average:62.423; most accessible tissue: Minghui63 flower, score: 77.232 | benign  |
0.555 |
DELETERIOUS | 0.03 |
| vg0224317158 | A -> DEL | LOC_Os02g40180.1 | N | frameshift_variant | Average:62.423; most accessible tissue: Minghui63 flower, score: 77.232 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224317158 | 2.18E-07 | 2.56E-08 | mr1227 | 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 |
| vg0224317158 | NA | 5.09E-07 | mr1583 | 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 |