Search for Variation information by Variation ID:
Detailed information for vg0519668538:
| Variant ID: vg0519668538 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19668538 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 63. )
Flanking Sequence (100 bp) in Reference Genome:
GACTGACGTCGTCGGACCGCTCGCAGATCATCAGGTGGCGGCACCTCTGAAGGAGAAGGTCGTCAAGGAGGCGTCTGACGCTGCCACCACTAGTGGTGGC[G/A]
AAGCTCCGACCAAGGCGAGGAAATTCTCGTCTGTGCTCGGACATCGCCGCAAGGCAGCAACTCCCTCGGTAATTTCACCTTGTCGCTAGGTTATGTAGCA
Reverse complement sequence
TGCTACATAACCTAGCGACAAGGTGAAATTACCGAGGGAGTTGCTGCCTTGCGGCGATGTCCGAGCACAGACGAGAATTTCCTCGCCTTGGTCGGAGCTT[C/T]
GCCACCACTAGTGGTGGCAGCGTCAGACGCCTCCTTGACGACCTTCTCCTTCAGAGGTGCCGCCACCTGATGATCTGCGAGCGGTCCGACGACGTCAGTC
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 | 30.90% | 19.60% | 4.44% | 45.01% | NA |
| All Indica | 2759 | 16.20% | 10.70% | 6.42% | 66.73% | NA |
| All Japonica | 1512 | 63.40% | 26.40% | 0.07% | 10.19% | NA |
| Aus | 269 | 10.40% | 69.50% | 9.29% | 10.78% | NA |
| Indica I | 595 | 12.90% | 0.50% | 1.85% | 84.71% | NA |
| Indica II | 465 | 3.20% | 27.70% | 5.38% | 63.66% | NA |
| Indica III | 913 | 25.70% | 9.00% | 10.30% | 54.98% | NA |
| Indica Intermediate | 786 | 15.30% | 10.20% | 5.98% | 68.58% | NA |
| Temperate Japonica | 767 | 94.70% | 1.20% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 8.70% | 74.20% | 0.20% | 16.87% | NA |
| Japonica Intermediate | 241 | 78.00% | 6.60% | 0.00% | 15.35% | NA |
| VI/Aromatic | 96 | 5.20% | 19.80% | 5.21% | 69.79% | NA |
| Intermediate | 90 | 26.70% | 31.10% | 2.22% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519668538 | G -> DEL | LOC_Os05g33480.1 | N | frameshift_variant | Average:7.272; most accessible tissue: Callus, score: 26.935 | N | N | N | N |
| vg0519668538 | G -> A | LOC_Os05g33480.1 | missense_variant ; p.Glu276Lys; MODERATE | nonsynonymous_codon ; E276K | Average:7.272; most accessible tissue: Callus, score: 26.935 | benign  |
-0.96 |
TOLERATED | 0.29 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519668538 | 8.53E-09 | 8.53E-09 | mr1848 | 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 |