Search for Variation information by Variation ID:
Detailed information for vg0412274018:
| Variant ID: vg0412274018 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12274018 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
ACCACCTTTGCTGGGCCTCCCCTCTTTGACTTACTTCCTTCACCTTTACTTTTTGCTCGTTTGTATCTTGCTGCCCCACAGACAGGGCAGACATCCAAGT[C/T]
AGCGTATTCCTTGTAATACAATATGCAGTCGTTCGGACATGCATGAATTCTTCTGACCTCCAGGCCCAACGGACATAATACTTGCTTCGCTTCATATGTC
Reverse complement sequence
GACATATGAAGCGAAGCAAGTATTATGTCCGTTGGGCCTGGAGGTCAGAAGAATTCATGCATGTCCGAACGACTGCATATTGTATTACAAGGAATACGCT[G/A]
ACTTGGATGTCTGCCCTGTCTGTGGGGCAGCAAGATACAAACGAGCAAAAAGTAAAGGTGAAGGAAGTAAGTCAAAGAGGGGAGGCCCAGCAAAGGTGGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 18.00% | 0.57% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.50% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 49.30% | 49.90% | 0.79% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 81.10% | 18.30% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 6.20% | 93.30% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 38.20% | 60.20% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 27.10% | 60.40% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 27.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0412274018 | C -> T | LOC_Os04g21700.1 | missense_variant ; p.Asp234Asn; MODERATE | nonsynonymous_codon ; D234N | Average:45.091; most accessible tissue: Zhenshan97 root, score: 64.045 | benign  |
0.429 |
TOLERATED | 0.32 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412274018 | NA | 2.82E-08 | mr1993 | 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 |
| vg0412274018 | NA | 5.69E-08 | mr1510_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 |
| vg0412274018 | NA | 2.37E-07 | mr1510_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 |