Search for Variation information by Variation ID:
Detailed information for vg0515438605:
| Variant ID: vg0515438605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15438605 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTCCATGGCGACCTCAAAGTCGCGCTTGCTTGTATGGAGCAGCGCGCGGACCACCTCGCCGCGGTGTCCAAGCCCGCGGGTGGCGACGAGAGGCTCAGC[A/G]
CCTCCGTCCCGGACGCCCCAAGGCAGCGGATGGTCACGTGCGACGAGGTCCCGGTCAAGGAGGTTGCCCTGGGCGACGGCCCGTCCAAGACCACACGAAT
Reverse complement sequence
ATTCGTGTGGTCTTGGACGGGCCGTCGCCCAGGGCAACCTCCTTGACCGGGACCTCGTCGCACGTGACCATCCGCTGCCTTGGGGCGTCCGGGACGGAGG[T/C]
GCTGAGCCTCTCGTCGCCACCCGCGGGCTTGGACACCGCGGCGAGGTGGTCCGCGCGCTGCTCCATACAAGCAAGCGCGACTTTGAGGTCGCCATGGACG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.60% | 0.20% | 3.72% | 53.49% | NA |
| All Indica | 2759 | 23.80% | 0.30% | 5.11% | 70.82% | NA |
| All Japonica | 1512 | 78.60% | 0.00% | 0.46% | 20.97% | NA |
| Aus | 269 | 8.90% | 0.00% | 9.67% | 81.41% | NA |
| Indica I | 595 | 20.80% | 0.00% | 3.19% | 75.97% | NA |
| Indica II | 465 | 31.40% | 0.90% | 6.88% | 60.86% | NA |
| Indica III | 913 | 27.60% | 0.00% | 5.48% | 66.92% | NA |
| Indica Intermediate | 786 | 17.00% | 0.50% | 5.09% | 77.35% | NA |
| Temperate Japonica | 767 | 94.70% | 0.00% | 0.00% | 5.35% | NA |
| Tropical Japonica | 504 | 53.00% | 0.00% | 0.99% | 46.03% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.00% | 0.83% | 18.26% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 2.22% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515438605 | A -> DEL | LOC_Os05g26570.1 | N | frameshift_variant | Average:9.084; most accessible tissue: Callus, score: 20.944 | N | N | N | N |
| vg0515438605 | A -> G | LOC_Os05g26570.1 | missense_variant ; p.Thr768Ala; MODERATE | nonsynonymous_codon ; T768A | Average:9.084; most accessible tissue: Callus, score: 20.944 | benign  |
0.111 |
TOLERATED | 0.15 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515438605 | 3.70E-06 | 3.70E-06 | mr1260 | 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 |