Search for Variation information by Variation ID:
Detailed information for vg1215236436:
| Variant ID: vg1215236436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15236436 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 115. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTTCACAGATTCTTTGGCTTTTATCTACTTTGAAAGATTATGGTCTTACTTTTGAGAAAGTACCTCTCTTTTGTGATAATACTAGTGCTATCAATATT[A/G]
CTAAGAATCCTGTTCAACACTCACGCACAAAGCACATTGATATTGGTTTTCACTTTTTGAGGGATCATGTTGAGAAAGGAGATGTTGAATTGCAGTTTTT
Reverse complement sequence
AAAAACTGCAATTCAACATCTCCTTTCTCAACATGATCCCTCAAAAAGTGAAAACCAATATCAATGTGCTTTGTGCGTGAGTGTTGAACAGGATTCTTAG[T/C]
AATATTGATAGCACTAGTATTATCACAAAAGAGAGGTACTTTCTCAAAAGTAAGACCATAATCTTTCAAAGTAGATAAAAGCCAAAGAATCTGTGAACAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.90% | 20.40% | 35.67% | 21.96% | NA |
| All Indica | 2759 | 4.00% | 26.80% | 45.23% | 24.03% | NA |
| All Japonica | 1512 | 57.70% | 13.80% | 20.11% | 8.33% | NA |
| Aus | 269 | 7.10% | 0.00% | 19.33% | 73.61% | NA |
| Indica I | 595 | 2.70% | 8.10% | 66.05% | 23.19% | NA |
| Indica II | 465 | 4.30% | 55.50% | 19.57% | 20.65% | NA |
| Indica III | 913 | 2.80% | 21.50% | 48.19% | 27.49% | NA |
| Indica Intermediate | 786 | 6.00% | 30.20% | 41.22% | 22.65% | NA |
| Temperate Japonica | 767 | 87.00% | 5.10% | 4.95% | 3.00% | NA |
| Tropical Japonica | 504 | 11.90% | 32.30% | 41.87% | 13.89% | NA |
| Japonica Intermediate | 241 | 60.60% | 2.90% | 22.82% | 13.69% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 50.00% | 38.54% | NA |
| Intermediate | 90 | 27.80% | 18.90% | 37.78% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215236436 | A -> DEL | LOC_Os12g26150.1 | N | frameshift_variant | Average:8.834; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1215236436 | A -> G | LOC_Os12g26150.1 | missense_variant ; p.Thr1260Ala; MODERATE | nonsynonymous_codon ; T1260A | Average:8.834; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
-0.468 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215236436 | 7.77E-07 | 1.12E-07 | mr1706 | 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 |
| vg1215236436 | NA | 5.04E-06 | mr1827_2 | Jap_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 |