Search for Variation information by Variation ID:
Detailed information for vg0112525167:
| Variant ID: vg0112525167 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12525167 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACTCGTGGCTATCGTGTACTTATTTTGGGGACTAACAAAATCGTGGAGACTTGCGAAGTTTCTTTTGATGAGGCTAGTCTAGATACTAGACCCGATATT[G/A]
CAGGTACACTGTCACAGGTTCAGGGGGAGGATGGTCATATTTTTGAAGACGAGAGCGACAACGACAACGACGACGACGAGGTCGGCTCGGCCGGTCAGAC
Reverse complement sequence
GTCTGACCGGCCGAGCCGACCTCGTCGTCGTCGTTGTCGTTGTCGCTCTCGTCTTCAAAAATATGACCATCCTCCCCCTGAACCTGTGACAGTGTACCTG[C/T]
AATATCGGGTCTAGTATCTAGACTAGCCTCATCAAAAGAAACTTCGCAAGTCTCCACGATTTTGTTAGTCCCCAAAATAAGTACACGATAGCCACGAGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.50% | 1.20% | 2.35% | 0.00% | NA |
| All Indica | 2759 | 94.00% | 2.00% | 3.95% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 80.00% | 5.60% | 14.41% | 0.00% | NA |
| Indica III | 913 | 97.60% | 1.30% | 1.10% | 0.00% | NA |
| Indica Intermediate | 786 | 93.90% | 2.30% | 3.82% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0112525167 | G -> A | LOC_Os01g22270.1 | missense_variant ; p.Ala829Thr; MODERATE | nonsynonymous_codon ; A829T | Average:27.407; most accessible tissue: Zhenshan97 panicle, score: 49.416 | possibly damaging  |
1.547 |
TOLERATED | 0.21 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0112525167 | 4.49E-06 | NA | mr1619 | 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 |