Search for Variation information by Variation ID:
Detailed information for vg1211533655:
| Variant ID: vg1211533655 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11533655 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 177. )
Flanking Sequence (100 bp) in Reference Genome:
AGACCGCTCCCAACAACGGATGTGGTCAAGCTGACGGAGCAATGCAGCAATGTGATACTCCACAAGCTCCCGGAGAAGAAGAAAGATCCGGGGTGTCCTA[T/C]
GATCACCTGCTCGATCAGGGCACATCAGTTCGACCAGGCCTTATGCAATCTTGGAGTCAGTGTCAACGTCATGCCAAAGGACGTCTTTGACAAGCTCAAC
Reverse complement sequence
GTTGAGCTTGTCAAAGACGTCCTTTGGCATGACGTTGACACTGACTCCAAGATTGCATAAGGCCTGGTCGAACTGATGTGCCCTGATCGAGCAGGTGATC[A/G]
TAGGACACCCCGGATCTTTCTTCTTCTCCGGGAGCTTGTGGAGTATCACATTGCTGCATTGCTCCGTCAGCTTGACCACATCCGTTGTTGGGAGCGGTCT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.50% | 13.40% | 7.89% | 17.25% | NA |
| All Indica | 2759 | 59.50% | 19.90% | 6.89% | 13.66% | NA |
| All Japonica | 1512 | 62.70% | 4.80% | 9.46% | 23.08% | NA |
| Aus | 269 | 75.50% | 0.40% | 8.92% | 15.24% | NA |
| Indica I | 595 | 70.10% | 3.00% | 4.71% | 22.18% | NA |
| Indica II | 465 | 49.00% | 32.90% | 5.81% | 12.26% | NA |
| Indica III | 913 | 57.90% | 22.00% | 9.09% | 10.95% | NA |
| Indica Intermediate | 786 | 59.50% | 22.60% | 6.62% | 11.20% | NA |
| Temperate Japonica | 767 | 90.50% | 0.70% | 1.69% | 7.17% | NA |
| Tropical Japonica | 504 | 29.20% | 11.70% | 19.44% | 39.68% | NA |
| Japonica Intermediate | 241 | 44.40% | 3.30% | 13.28% | 39.00% | NA |
| VI/Aromatic | 96 | 51.00% | 1.00% | 9.38% | 38.54% | NA |
| Intermediate | 90 | 71.10% | 8.90% | 7.78% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211533655 | T -> C | LOC_Os12g19790.1 | missense_variant ; p.Met214Thr; MODERATE | nonsynonymous_codon ; M214T | Average:8.676; most accessible tissue: Callus, score: 33.38 | benign  |
-0.525 |
TOLERATED | 1.00 |
| vg1211533655 | T -> DEL | LOC_Os12g19790.1 | N | frameshift_variant | Average:8.676; most accessible tissue: Callus, score: 33.38 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211533655 | 4.54E-06 | 4.54E-06 | mr1333_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 |
| vg1211533655 | NA | 2.81E-07 | mr1350_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 |
| vg1211533655 | 4.17E-06 | NA | mr1362_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 |
| vg1211533655 | NA | 3.80E-06 | mr1425_2 | 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 |
| vg1211533655 | NA | 7.68E-06 | mr1686_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 |
| vg1211533655 | NA | 2.42E-06 | mr1830_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 |