Search for Variation information by Variation ID:
Detailed information for vg0519675117:
| Variant ID: vg0519675117 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19675117 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTCTTCTCGACAACGCGTACTCGCTTGCCTTTTTCAAACGTCATGTGCTTCTCGAGCGACTTTTTGAAAACAAGGCAATCCTCCAGAGAATGTCTGTCC[G/A]
TTTTGTGTATGGGGCACCATGATTTTTTTGTATCGCTGGCTTGTGGGTCTGGGCGCTTGGGAGGGTTCGCGTATTCTGCTGCGAGGACTTCCGCTTGAGC
Reverse complement sequence
GCTCAAGCGGAAGTCCTCGCAGCAGAATACGCGAACCCTCCCAAGCGCCCAGACCCACAAGCCAGCGATACAAAAAAATCATGGTGCCCCATACACAAAA[C/T]
GGACAGACATTCTCTGGAGGATTGCCTTGTTTTCAAAAAGTCGCTCGAGAAGCACATGACGTTTGAAAAAGGCAAGCGAGTACGCGTTGTCGAGAAGAAC
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 | 93.80% | 0.30% | 1.54% | 4.30% | NA |
| All Indica | 2759 | 95.10% | 0.40% | 2.03% | 2.46% | NA |
| All Japonica | 1512 | 91.60% | 0.20% | 0.60% | 7.61% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.20% | 1.85% | 0.50% | NA |
| Indica II | 465 | 89.20% | 0.40% | 3.44% | 6.88% | NA |
| Indica III | 913 | 97.50% | 0.70% | 0.77% | 1.10% | NA |
| Indica Intermediate | 786 | 93.90% | 0.40% | 2.80% | 2.93% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.26% | 3.26% | NA |
| Tropical Japonica | 504 | 85.50% | 0.40% | 0.60% | 13.49% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.40% | 1.66% | 9.13% | NA |
| VI/Aromatic | 96 | 85.40% | 1.00% | 2.08% | 11.46% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 5.56% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519675117 | G -> DEL | LOC_Os05g33490.1 | N | frameshift_variant | Average:9.544; most accessible tissue: Callus, score: 16.454 | N | N | N | N |
| vg0519675117 | G -> A | LOC_Os05g33490.1 | missense_variant ; p.Thr721Met; MODERATE | nonsynonymous_codon ; T721M | Average:9.544; most accessible tissue: Callus, score: 16.454 | benign  |
0.748 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519675117 | 6.40E-06 | 6.40E-06 | mr1427_2 | Jap_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 |
| vg0519675117 | 3.74E-06 | NA | mr1665_2 | 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 |