Search for Variation information by Variation ID:
Detailed information for vg0613080964:
| Variant ID: vg0613080964 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 13080964 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 77. )
Flanking Sequence (100 bp) in Reference Genome:
CACTAAGAACCTTTGCGTAAACCTGATGGGCTTCTTAGGTGTATATGGGAAGTCCAAAGATACACTCGAAGCATGCAATGATCTCAAGCATATGGAACAA[T/C]
ACGAGGGCCTTCATCCAGAACCGAATGAGAAAGGAAGCCATTACTTGAGTCCGGCGAGCTACACCCTGAGCAAGGAAGAGAAGGATAGTATGTTTCAATG
Reverse complement sequence
CATTGAAACATACTATCCTTCTCTTCCTTGCTCAGGGTGTAGCTCGCCGGACTCAAGTAATGGCTTCCTTTCTCATTCGGTTCTGGATGAAGGCCCTCGT[A/G]
TTGTTCCATATGCTTGAGATCATTGCATGCTTCGAGTGTATCTTTGGACTTCCCATATACACCTAAGAAGCCCATCAGGTTTACGCAAAGGTTCTTAGTG
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 | 50.30% | 37.50% | 11.38% | 0.83% | NA |
| All Indica | 2759 | 75.20% | 11.70% | 12.43% | 0.69% | NA |
| All Japonica | 1512 | 9.20% | 88.30% | 1.32% | 1.19% | NA |
| Aus | 269 | 23.40% | 25.30% | 51.30% | 0.00% | NA |
| Indica I | 595 | 77.30% | 8.20% | 12.10% | 2.35% | NA |
| Indica II | 465 | 56.30% | 27.70% | 15.70% | 0.22% | NA |
| Indica III | 913 | 87.00% | 1.80% | 11.17% | 0.11% | NA |
| Indica Intermediate | 786 | 71.10% | 16.30% | 12.21% | 0.38% | NA |
| Temperate Japonica | 767 | 0.90% | 95.30% | 1.69% | 2.09% | NA |
| Tropical Japonica | 504 | 22.00% | 77.20% | 0.60% | 0.20% | NA |
| Japonica Intermediate | 241 | 8.70% | 89.20% | 1.66% | 0.41% | NA |
| VI/Aromatic | 96 | 67.70% | 4.20% | 28.12% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 46.70% | 11.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0613080964 | T -> C | LOC_Os06g22510.1 | missense_variant ; p.Tyr341His; MODERATE | nonsynonymous_codon ; Y341R | Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447 | possibly damaging  |
-1.618 |
TOLERATED | 1.00 |
| vg0613080964 | T -> C | LOC_Os06g22510.1 | missense_variant ; p.Tyr341His; MODERATE | nonsynonymous_codon ; Y341H | Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447 | possibly damaging |
-1.52 |
DELETERIOUS | 0.03 |
| vg0613080964 | T -> DEL | LOC_Os06g22510.1 | N | frameshift_variant | Average:20.247; most accessible tissue: Zhenshan97 panicle, score: 28.447 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0613080964 | NA | 1.30E-06 | mr1886 | 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 |
| vg0613080964 | NA | 2.01E-09 | mr1979 | 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 |