Search for Variation information by Variation ID:
Detailed information for vg1005078467:
| Variant ID: vg1005078467 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5078467 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 84. )
Flanking Sequence (100 bp) in Reference Genome:
TACATAGCCTGACCAGCCGCCTATGCTCTTGGTCTTGAAGTCATATTTGTTCTTTGTATTCAAACTCATAGGGTTGGCCGATGAGGTGACATCCAGACCC[G/A]
TGATCATGCTGATATCTATGAGAGTTGGGGTCATCGGCCCTTGATTAAACAAAAAGGCATTGATGGTGTTTGACCAGAAGTAAGAAGCAGATGCCATCAG
Reverse complement sequence
CTGATGGCATCTGCTTCTTACTTCTGGTCAAACACCATCAATGCCTTTTTGTTTAATCAAGGGCCGATGACCCCAACTCTCATAGATATCAGCATGATCA[C/T]
GGGTCTGGATGTCACCTCATCGGCCAACCCTATGAGTTTGAATACAAAGAACAAATATGACTTCAAGACCAAGAGCATAGGCGGCTGGTCAGGCTATGTA
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 | 92.30% | 1.70% | 2.58% | 3.45% | NA |
| All Indica | 2759 | 95.30% | 2.30% | 2.46% | 0.00% | NA |
| All Japonica | 1512 | 87.20% | 0.20% | 2.98% | 9.59% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.10% | 4.50% | 3.36% | 0.00% | NA |
| Indica II | 465 | 96.30% | 1.50% | 2.15% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.30% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 3.30% | 4.45% | 0.00% | NA |
| Temperate Japonica | 767 | 88.10% | 0.40% | 2.48% | 9.00% | NA |
| Tropical Japonica | 504 | 88.10% | 0.00% | 3.97% | 7.94% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 2.49% | 14.94% | NA |
| VI/Aromatic | 96 | 65.60% | 8.30% | 7.29% | 18.75% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1005078467 | G -> A | LOC_Os10g09410.1 | missense_variant ; p.Thr156Met; MODERATE | nonsynonymous_codon ; T156M | Average:19.562; most accessible tissue: Callus, score: 28.606 | benign  |
1.252 |
DELETERIOUS | 0.01 |
| vg1005078467 | G -> DEL | LOC_Os10g09410.1 | N | frameshift_variant | Average:19.562; most accessible tissue: Callus, score: 28.606 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005078467 | NA | 5.52E-06 | mr1371_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 |
| vg1005078467 | 1.43E-06 | 1.43E-06 | mr1979_2 | 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 |