Search for Variation information by Variation ID:
Detailed information for vg0118482824:
| Variant ID: vg0118482824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18482824 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCGCAGGAGCTGGAGGAAGAAGAAATTCATCCTTCAGAAATTCCATTCGAATTCGAGGAGAATCTTTTCAAATTTTGTTGGAACACCTCAAATTATTCC[T/G]
GCGAGAAGAGACCACCGACCAAGGTCAATTCTGATGAACCTCTCGATAAAGCTATGCTTAAAGAGACGGTGAAGAAGTTGACCACCATCATGAGTAACAA
Reverse complement sequence
TTGTTACTCATGATGGTGGTCAACTTCTTCACCGTCTCTTTAAGCATAGCTTTATCGAGAGGTTCATCAGAATTGACCTTGGTCGGTGGTCTCTTCTCGC[A/C]
GGAATAATTTGAGGTGTTCCAACAAAATTTGAAAAGATTCTCCTCGAATTCGAATGGAATTTCTGAAGGATGAATTTCTTCTTCCTCCAGCTCCTGCGAC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.40% | 1.20% | 2.45% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 89.60% | 2.90% | 7.47% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 82.10% | 5.30% | 12.52% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 1.20% | 5.39% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 10.00% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118482824 | T -> G | LOC_Os01g33580.1 | missense_variant ; p.Cys150Gly; MODERATE | nonsynonymous_codon ; C150G | Average:39.032; most accessible tissue: Minghui63 flower, score: 52.791 | benign  |
1.254 |
TOLERATED | 0.13 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0118482824 | NA | 4.63E-06 | mr1607 | 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 |
| vg0118482824 | NA | 1.90E-06 | mr1712_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 |
| vg0118482824 | 5.26E-06 | 2.49E-08 | mr1946_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 |
| vg0118482824 | 5.26E-06 | 2.49E-08 | mr1948_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 |