Search for Variation information by Variation ID:
Detailed information for vg0111184479:
| Variant ID: vg0111184479 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 11184479 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCGATATAGGTTTTGGTGTAGGATCAGTCTCTTCAGTACCATCGAACTCCGCCTTCATCTTGCGGTACTTGTGATTTGTGCGTAGGAACCGCCAGTGCC[G/A]
CATGTACACAAGCTTGTTGGAACCCGGGAGATACCTATAGTACGTTCCATTCAAGCAGATCACACATCCTGTTTTACCTTTAATTTGACCTGAAACTGAA
Reverse complement sequence
TTCAGTTTCAGGTCAAATTAAAGGTAAAACAGGATGTGTGATCTGCTTGAATGGAACGTACTATAGGTATCTCCCGGGTTCCAACAAGCTTGTGTACATG[C/T]
GGCACTGGCGGTTCCTACGCACAAATCACAAGTACCGCAAGATGAAGGCGGAGTTCGATGGTACTGAAGAGACTGATCCTACACCAAAACCTATATCGGG
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 | 89.00% | 1.20% | 7.24% | 2.58% | NA |
| All Indica | 2759 | 84.50% | 1.80% | 10.04% | 3.70% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.40% | 0.13% | NA |
| Aus | 269 | 80.30% | 1.50% | 15.24% | 2.97% | NA |
| Indica I | 595 | 85.70% | 0.70% | 10.92% | 2.69% | NA |
| Indica II | 465 | 83.20% | 0.60% | 11.18% | 4.95% | NA |
| Indica III | 913 | 85.70% | 3.20% | 7.12% | 4.05% | NA |
| Indica Intermediate | 786 | 82.80% | 1.80% | 12.09% | 3.31% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 8.33% | 6.25% | NA |
| Intermediate | 90 | 83.30% | 1.10% | 11.11% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0111184479 | G -> A | LOC_Os01g19720.1 | missense_variant ; p.Arg288Trp; MODERATE | nonsynonymous_codon ; R288W | Average:17.033; most accessible tissue: Zhenshan97 root, score: 22.162 | probably damaging  |
3.346 |
DELETERIOUS | 0.04 |
| vg0111184479 | G -> DEL | LOC_Os01g19720.1 | N | frameshift_variant | Average:17.033; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0111184479 | 2.69E-06 | NA | mr1795 | 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 |