Search for Variation information by Variation ID:
Detailed information for vg1218447354:
| Variant ID: vg1218447354 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18447354 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAAATGGTGGTTCAAAAGAAGCAGGTTGTTCCAACTGCAACGAGCAAAAATCTGCAACCTGCAGTCTGGAGAGCTTTGACAGAATAACTTCGGGAATCT[C/G]
TCTGATAGGATTTGACCTGAGAAGCAAGTACTGCAACTTAAAAAGGAGTCCAAGCTCTTGAGGCAAGTCTTTGATTTTATTATCTGATAAATTCAGGTAA
Reverse complement sequence
TTACCTGAATTTATCAGATAATAAAATCAAAGACTTGCCTCAAGAGCTTGGACTCCTTTTTAAGTTGCAGTACTTGCTTCTCAGGTCAAATCCTATCAGA[G/C]
AGATTCCCGAAGTTATTCTGTCAAAGCTCTCCAGACTGCAGGTTGCAGATTTTTGCTCGTTGCAGTTGGAACAACCTGCTTCTTTTGAACCACCATTTGG
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 | 44.50% | 2.00% | 4.59% | 48.94% | NA |
| All Indica | 2759 | 20.70% | 0.00% | 3.77% | 75.53% | NA |
| All Japonica | 1512 | 88.00% | 6.20% | 4.23% | 1.65% | NA |
| Aus | 269 | 20.10% | 0.00% | 17.47% | 62.45% | NA |
| Indica I | 595 | 39.50% | 0.00% | 3.70% | 56.81% | NA |
| Indica II | 465 | 9.20% | 0.20% | 4.09% | 86.45% | NA |
| Indica III | 913 | 10.80% | 0.00% | 3.29% | 85.87% | NA |
| Indica Intermediate | 786 | 24.60% | 0.00% | 4.20% | 71.25% | NA |
| Temperate Japonica | 767 | 81.00% | 11.20% | 6.52% | 1.30% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 1.59% | 0.79% | NA |
| Japonica Intermediate | 241 | 90.00% | 2.90% | 2.49% | 4.56% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 0.00% | 17.71% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 2.22% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218447354 | C -> DEL | LOC_Os12g30720.1 | N | frameshift_variant | Average:23.222; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1218447354 | C -> G | LOC_Os12g30720.1 | missense_variant ; p.Glu619Gln; MODERATE | nonsynonymous_codon ; E619Q | Average:23.222; most accessible tissue: Zhenshan97 panicle, score: 65.386 | benign  |
1.135 |
TOLERATED | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218447354 | 1.51E-07 | 4.10E-07 | mr1458_2 | Jap_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 |