Search for Variation information by Variation ID:
Detailed information for vg1209158100:
| Variant ID: vg1209158100 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9158100 |
| Reference Allele: C | Alternative Allele: G,A |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, C: 0.24, A: 0.04, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
ATATTGCCTTTGAAGCTCAGGGGACATAGTAGCAAGCATGAGACAGCTTATATCAAAGTATTCATTGCATCGCATTTCATGCTCCCTACGTTGAGCAGCA[C/G,A]
GAGCATTGTTGGGCAAGTCAGCTAGAAAAGGTTGTGTAAGCACAAACTCTTTGTGCTCTTGCCTGAGAACAATTCTCAGGTTGCGATACCAATCCATGAA
Reverse complement sequence
TTCATGGATTGGTATCGCAACCTGAGAATTGTTCTCAGGCAAGAGCACAAAGAGTTTGTGCTTACACAACCTTTTCTAGCTGACTTGCCCAACAATGCTC[G/C,T]
TGCTGCTCAACGTAGGGAGCATGAAATGCGATGCAATGAATACTTTGATATAAGCTGTCTCATGCTTGCTACTATGTCCCCTGAGCTTCAAAGGCAATAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.00% | 5.00% | 7.13% | 53.94% | A: 0.02% |
| All Indica | 2759 | 3.40% | 6.40% | 8.95% | 81.23% | A: 0.04% |
| All Japonica | 1512 | 94.40% | 3.00% | 0.33% | 2.25% | NA |
| Aus | 269 | 4.10% | 2.60% | 23.05% | 70.26% | NA |
| Indica I | 595 | 2.70% | 0.30% | 8.07% | 88.91% | NA |
| Indica II | 465 | 4.50% | 12.70% | 9.03% | 73.76% | NA |
| Indica III | 913 | 2.40% | 4.60% | 9.64% | 83.24% | A: 0.11% |
| Indica Intermediate | 786 | 4.30% | 9.40% | 8.78% | 77.48% | NA |
| Temperate Japonica | 767 | 92.70% | 5.60% | 0.52% | 1.17% | NA |
| Tropical Japonica | 504 | 95.60% | 0.60% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 16.67% | 57.29% | NA |
| Intermediate | 90 | 54.40% | 4.40% | 7.78% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209158100 | C -> A | LOC_Os12g16060.1 | missense_variant ; p.Arg121Leu; MODERATE | nonsynonymous_codon ; R121L | Average:8.335; most accessible tissue: Callus, score: 19.445 | benign  |
-0.782 |
TOLERATED | 0.15 |
| vg1209158100 | C -> DEL | LOC_Os12g16060.1 | N | frameshift_variant | Average:8.335; most accessible tissue: Callus, score: 19.445 | N | N | N | N |
| vg1209158100 | C -> G | LOC_Os12g16060.1 | missense_variant ; p.Arg121Pro; MODERATE | nonsynonymous_codon ; R121P | Average:8.335; most accessible tissue: Callus, score: 19.445 | possibly damaging |
-1.911 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209158100 | 3.57E-06 | NA | mr1167_2 | 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 |