Search for Variation information by Variation ID:
Detailed information for vg0619939165:
| Variant ID: vg0619939165 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 19939165 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, T: 0.30, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
AAATTTAGCAAGCAAAAATAAGTCATACCCGCACAAATAGGCTCTCCACAGCCACATAGCTTTCGCCGAACTCGTTCAGTTCGGTGAAAAGCCCAAGGCC[A/T]
TCGGTCGACGCTATGACCTGGCACACCCCGTCCACGAACGGAATGATCTCCGGTCGCGTGGCAAAGTCGGCGGGGACGAAATGTGGGGCGGTAATCGTCA
Reverse complement sequence
TGACGATTACCGCCCCACATTTCGTCCCCGCCGACTTTGCCACGCGACCGGAGATCATTCCGTTCGTGGACGGGGTGTGCCAGGTCATAGCGTCGACCGA[T/A]
GGCCTTGGGCTTTTCACCGAACTGAACGAGTTCGGCGAAAGCTATGTGGCTGTGGAGAGCCTATTTGTGCGGGTATGACTTATTTTTGCTTGCTAAATTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.50% | 33.00% | 0.59% | 0.89% | NA |
| All Indica | 2759 | 95.00% | 4.80% | 0.14% | 0.04% | NA |
| All Japonica | 1512 | 4.70% | 92.10% | 0.53% | 2.65% | NA |
| Aus | 269 | 94.80% | 0.00% | 5.20% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 92.50% | 6.90% | 0.43% | 0.22% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.60% | 8.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 96.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 7.10% | 84.30% | 0.79% | 7.74% | NA |
| Japonica Intermediate | 241 | 5.00% | 93.40% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 36.70% | 2.22% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0619939165 | A -> T | LOC_Os06g34250.1 | missense_variant ; p.Asp451Glu; MODERATE | nonsynonymous_codon ; D451K | Average:58.515; most accessible tissue: Minghui63 flag leaf, score: 81.052 | benign  |
0.108 |
TOLERATED | 0.13 |
| vg0619939165 | A -> T | LOC_Os06g34250.1 | missense_variant ; p.Asp451Glu; MODERATE | nonsynonymous_codon ; D451E | Average:58.515; most accessible tissue: Minghui63 flag leaf, score: 81.052 | benign |
-0.226 |
TOLERATED | 1.00 |
| vg0619939165 | A -> DEL | LOC_Os06g34250.1 | N | frameshift_variant | Average:58.515; most accessible tissue: Minghui63 flag leaf, score: 81.052 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0619939165 | NA | 3.31E-07 | mr1245 | 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 |
| vg0619939165 | NA | 3.23E-06 | mr1532 | 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 |
| vg0619939165 | 1.62E-06 | NA | mr1784 | 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 |