Search for Variation information by Variation ID:
Detailed information for vg1209716081:
| Variant ID: vg1209716081 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9716081 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTGAAATCCAGCACCCCCAACTACGCATGGCTTGCTCTTGTTCGGTTGGGGTTTGAGGAAGAAGATATAGCAGAATAGGGCAAAATGTGGCCTGACGCC[C/T]
ATAAAAGCTTCGCAGGCATGTATGAAGTTGGCAATATGAACTATGGAATTCGGGTTTAGGTGATGCAAACTAATCCCATAGAAATCCAAAATCCACCGGA
Reverse complement sequence
TCCGGTGGATTTTGGATTTCTATGGGATTAGTTTGCATCACCTAAACCCGAATTCCATAGTTCATATTGCCAACTTCATACATGCCTGCGAAGCTTTTAT[G/A]
GGCGTCAGGCCACATTTTGCCCTATTCTGCTATATCTTCTTCCTCAAACCCCAACCGAACAAGAGCAAGCCATGCGTAGTTGGGGGTGCTGGATTTCAAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.90% | 6.60% | 0.63% | 29.86% | NA |
| All Indica | 2759 | 39.40% | 11.10% | 1.01% | 48.50% | NA |
| All Japonica | 1512 | 97.10% | 0.10% | 0.00% | 2.78% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 63.70% | 0.70% | 1.51% | 34.12% | NA |
| Indica II | 465 | 24.70% | 30.10% | 0.22% | 44.95% | NA |
| Indica III | 913 | 29.20% | 7.30% | 0.88% | 62.54% | NA |
| Indica Intermediate | 786 | 41.50% | 12.10% | 1.27% | 45.17% | NA |
| Temperate Japonica | 767 | 95.20% | 0.10% | 0.00% | 4.69% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 2.08% | 18.75% | NA |
| Intermediate | 90 | 83.30% | 3.30% | 0.00% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209716081 | C -> DEL | LOC_Os12g16960.1 | N | frameshift_variant | Average:52.377; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg1209716081 | C -> T | LOC_Os12g16960.1 | missense_variant ; p.Met107Ile; MODERATE | nonsynonymous_codon ; M107L | Average:52.377; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | probably damaging  |
-2.661 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209716081 | 1.60E-06 | 8.99E-07 | mr1182_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 |