Search for Variation information by Variation ID:
Detailed information for vg1114444146:
| Variant ID: vg1114444146 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14444146 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 66. )
Flanking Sequence (100 bp) in Reference Genome:
CGCACCTGAGTCAAGCAAGAAGAAGAGTCGCAAGAGTGGGAAAAGGAAAGCTCAAACAGAAGTCCTCGTAGCAGAATACGCGGAACCACCCAAGCACCCA[G/T]
ACCCACAAAGGGACGATACGAAGAAAATATGGTGCCTTATACACAAATCGGACAAGCACTCCCTAGAAGCTTGTTTCGTTTTCAAAAAGCCACTCGCAAA
Reverse complement sequence
TTTGCGAGTGGCTTTTTGAAAACGAAACAAGCTTCTAGGGAGTGCTTGTCCGATTTGTGTATAAGGCACCATATTTTCTTCGTATCGTCCCTTTGTGGGT[C/A]
TGGGTGCTTGGGTGGTTCCGCGTATTCTGCTACGAGGACTTCTGTTTGAGCTTTCCTTTTCCCACTCTTGCGACTCTTCTTCTTGCTTGACTCAGGTGCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.80% | 24.40% | 1.97% | 9.86% | NA |
| All Indica | 2759 | 41.10% | 41.00% | 3.23% | 14.72% | NA |
| All Japonica | 1512 | 98.60% | 0.70% | 0.13% | 0.53% | NA |
| Aus | 269 | 81.40% | 1.10% | 0.37% | 17.10% | NA |
| Indica I | 595 | 37.50% | 56.10% | 0.34% | 6.05% | NA |
| Indica II | 465 | 62.60% | 35.90% | 0.43% | 1.08% | NA |
| Indica III | 913 | 26.70% | 34.30% | 8.98% | 30.01% | NA |
| Indica Intermediate | 786 | 47.80% | 40.20% | 0.38% | 11.58% | NA |
| Temperate Japonica | 767 | 99.20% | 0.40% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 97.60% | 1.40% | 0.20% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 10.00% | 1.11% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114444146 | G -> T | LOC_Os11g25340.1 | missense_variant ; p.Asp269Tyr; MODERATE | nonsynonymous_codon ; D269Y | Average:18.539; most accessible tissue: Minghui63 young leaf, score: 36.684 | probably damaging  |
2.794 |
DELETERIOUS | 0.02 |
| vg1114444146 | G -> DEL | LOC_Os11g25340.1 | N | frameshift_variant | Average:18.539; most accessible tissue: Minghui63 young leaf, score: 36.684 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1114444146 | NA | 1.05E-06 | mr1154_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 |