Search for Variation information by Variation ID:
Detailed information for vg0807809853:
| Variant ID: vg0807809853 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7809853 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGTATTGAGTAAGTTCACAGTTACCGTTATGTGGTCGACGGCACTGTCGACCGATGTTGGATTTTCCACCAACTCAGTTGATGCGCAACTGCTTTGTTTT[C/T]
GGGTGGGACTTCCTAACTCTTCGTGCGCAGCAGCAACGGCGGCCTGGGGGTTCTGTTGCTCTTCTCGAATCTCTTGCCTAATCTTGGCCCTCATCGACTC
Reverse complement sequence
GAGTCGATGAGGGCCAAGATTAGGCAAGAGATTCGAGAAGAGCAACAGAACCCCCAGGCCGCCGTTGCTGCTGCGCACGAAGAGTTAGGAAGTCCCACCC[G/A]
AAAACAAAGCAGTTGCGCATCAACTGAGTTGGTGGAAAATCCAACATCGGTCGACAGTGCCGTCGACCACATAACGGTAACTGTGAACTTACTCAATACA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.60% | 20.90% | 8.48% | 42.02% | NA |
| All Indica | 2759 | 33.80% | 2.20% | 5.44% | 58.57% | NA |
| All Japonica | 1512 | 23.50% | 59.40% | 11.18% | 5.89% | NA |
| Aus | 269 | 12.60% | 1.50% | 4.83% | 81.04% | NA |
| Indica I | 595 | 4.50% | 2.40% | 3.53% | 89.58% | NA |
| Indica II | 465 | 55.70% | 4.90% | 1.72% | 37.63% | NA |
| Indica III | 913 | 46.20% | 0.70% | 9.09% | 44.03% | NA |
| Indica Intermediate | 786 | 28.60% | 2.20% | 4.83% | 64.38% | NA |
| Temperate Japonica | 767 | 34.60% | 55.40% | 7.82% | 2.22% | NA |
| Tropical Japonica | 504 | 5.40% | 74.80% | 8.93% | 10.91% | NA |
| Japonica Intermediate | 241 | 26.60% | 39.80% | 26.56% | 7.05% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 61.46% | 27.08% | NA |
| Intermediate | 90 | 18.90% | 28.90% | 11.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0807809853 | C -> T | LOC_Os08g13150.1 | missense_variant ; p.Arg923Gln; MODERATE | nonsynonymous_codon ; R923Q | Average:22.067; most accessible tissue: Minghui63 young leaf, score: 50.756 | benign  |
-0.862 |
TOLERATED | 1.00 |
| vg0807809853 | C -> DEL | LOC_Os08g13150.1 | N | frameshift_variant | Average:22.067; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0807809853 | 1.02E-06 | NA | mr1017 | 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 |