Search for Variation information by Variation ID:
Detailed information for vg0136979159:
| Variant ID: vg0136979159 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36979159 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTGCAGCGGCTGCATCTTCATGGGCCCATATTGCCTCCTTGCCGATGTACCCTGCGGTGCCCAGCCGATGCGGGTGCTCATTCCGCTGTTGCAGTAGGC[G/A]
ATGTGCCTCGCTTGATTCTCTAAACTCTTGGGTGTTCTTGAGAGAGCAGAATTCCTCCCACACCGCTTCGGTTATTTGAGGGTATTCATCGAACGGCGTA
Reverse complement sequence
TACGCCGTTCGATGAATACCCTCAAATAACCGAAGCGGTGTGGGAGGAATTCTGCTCTCTCAAGAACACCCAAGAGTTTAGAGAATCAAGCGAGGCACAT[C/T]
GCCTACTGCAACAGCGGAATGAGCACCCGCATCGGCTGGGCACCGCAGGGTACATCGGCAAGGAGGCAATATGGGCCCATGAAGATGCAGCCGCTGCAGC
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 | 45.80% | 4.00% | 47.91% | 2.31% | NA |
| All Indica | 2759 | 15.70% | 6.90% | 73.72% | 3.73% | NA |
| All Japonica | 1512 | 98.20% | 0.00% | 1.46% | 0.33% | NA |
| Aus | 269 | 34.90% | 0.00% | 65.06% | 0.00% | NA |
| Indica I | 595 | 11.30% | 1.50% | 81.18% | 6.05% | NA |
| Indica II | 465 | 17.80% | 1.30% | 75.27% | 5.59% | NA |
| Indica III | 913 | 15.40% | 15.20% | 68.67% | 0.66% | NA |
| Indica Intermediate | 786 | 18.10% | 4.50% | 73.03% | 4.45% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 2.38% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 5.21% | 1.04% | NA |
| Intermediate | 90 | 67.80% | 1.10% | 31.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136979159 | G -> A | LOC_Os01g63740.1 | missense_variant ; p.Arg210Cys; MODERATE | nonsynonymous_codon ; R210C | Average:15.777; most accessible tissue: Zhenshan97 flower, score: 22.37 | probably damaging  |
3.187 |
DELETERIOUS | 0.00 |
| vg0136979159 | G -> DEL | LOC_Os01g63740.1 | N | frameshift_variant | Average:15.777; most accessible tissue: Zhenshan97 flower, score: 22.37 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136979159 | 3.90E-06 | 4.24E-06 | mr1438 | 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 |