Search for Variation information by Variation ID:
Detailed information for vg1213714850:
| Variant ID: vg1213714850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13714850 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCAGGAGAATCTGCAGCTGAAGAAGGACCTAGACGCGGTGGAGGCGCAGGTGTGTCAGCTCAAGGTCGCCCAGGGAGAGGTCTGCCGTCCCAAGCGCCGC[C/T]
GCGTCTGCCGCAGCCTGAAGATCACTGCCCGCAGGAGCACCTCCAGGCCTGAGCTTGTTCGTCAGTCCCTGGCGTGGACCTGCTTTGTGGAGACCCCTTG
Reverse complement sequence
CAAGGGGTCTCCACAAAGCAGGTCCACGCCAGGGACTGACGAACAAGCTCAGGCCTGGAGGTGCTCCTGCGGGCAGTGATCTTCAGGCTGCGGCAGACGC[G/A]
GCGGCGCTTGGGACGGCAGACCTCTCCCTGGGCGACCTTGAGCTGACACACCTGCGCCTCCACCGCGTCTAGGTCCTTCTTCAGCTGCAGATTCTCCTGA
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 | 64.60% | 14.60% | 17.10% | 3.72% | NA |
| All Indica | 2759 | 56.90% | 16.60% | 23.99% | 2.54% | NA |
| All Japonica | 1512 | 88.70% | 1.70% | 2.91% | 6.75% | NA |
| Aus | 269 | 21.90% | 56.10% | 21.93% | 0.00% | NA |
| Indica I | 595 | 45.20% | 9.40% | 40.17% | 5.21% | NA |
| Indica II | 465 | 52.00% | 26.00% | 21.08% | 0.86% | NA |
| Indica III | 913 | 65.20% | 15.80% | 16.32% | 2.74% | NA |
| Indica Intermediate | 786 | 58.90% | 17.40% | 22.39% | 1.27% | NA |
| Temperate Japonica | 767 | 89.00% | 1.60% | 2.09% | 7.30% | NA |
| Tropical Japonica | 504 | 95.60% | 0.80% | 1.39% | 2.18% | NA |
| Japonica Intermediate | 241 | 73.00% | 3.70% | 8.71% | 14.52% | NA |
| VI/Aromatic | 96 | 22.90% | 45.80% | 31.25% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 14.40% | 14.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1213714850 | C -> DEL | LOC_Os12g24110.1 | N | frameshift_variant | Average:38.399; most accessible tissue: Minghui63 young leaf, score: 69.4 | N | N | N | N |
| vg1213714850 | C -> T | LOC_Os12g24110.1 | missense_variant ; p.Arg231Cys; MODERATE | nonsynonymous_codon ; R231C | Average:38.399; most accessible tissue: Minghui63 young leaf, score: 69.4 | probably damaging  |
2.729 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213714850 | 2.26E-06 | NA | mr1932 | 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 |
| vg1213714850 | NA | 7.42E-06 | mr1932 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |