Search for Variation information by Variation ID:
Detailed information for vg1215734129:
| Variant ID: vg1215734129 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15734129 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, G: 0.12, others allele: 0.00, population size: 74. )
Flanking Sequence (100 bp) in Reference Genome:
GCACATCAACATAACTTTGGGCACCTCTAACAATCATCAGTAGCATTCGCAAGTAGTAAAGCTCACCAGCAGTTGGATGCACATAGTAAATTCTACCAAT[G/T]
TTTGGAGCAGGAGTTCGTGGGCGCCACACTCTAGATGATGGCTCCCATGTCCATTCTTTTGGAAATTCGCAGTATGTCAATGAATGAGCCTTAGGATATT
Reverse complement sequence
AATATCCTAAGGCTCATTCATTGACATACTGCGAATTTCCAAAAGAATGGACATGGGAGCCATCATCTAGAGTGTGGCGCCCACGAACTCCTGCTCCAAA[C/A]
ATTGGTAGAATTTACTATGTGCATCCAACTGCTGGTGAGCTTTACTACTTGCGAATGCTACTGATGATTGTTAGAGGTGCCCAAAGTTATGTTGATGTGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.70% | 9.30% | 0.36% | 61.66% | NA |
| All Indica | 2759 | 12.40% | 10.70% | 0.33% | 76.59% | NA |
| All Japonica | 1512 | 61.20% | 2.90% | 0.33% | 35.52% | NA |
| Aus | 269 | 14.10% | 2.60% | 0.74% | 82.53% | NA |
| Indica I | 595 | 16.30% | 7.90% | 0.67% | 75.13% | NA |
| Indica II | 465 | 22.40% | 8.80% | 0.00% | 68.82% | NA |
| Indica III | 913 | 1.60% | 12.90% | 0.22% | 85.21% | NA |
| Indica Intermediate | 786 | 16.00% | 11.30% | 0.38% | 72.26% | NA |
| Temperate Japonica | 767 | 92.60% | 0.30% | 0.00% | 7.17% | NA |
| Tropical Japonica | 504 | 12.50% | 6.20% | 0.79% | 80.56% | NA |
| Japonica Intermediate | 241 | 63.50% | 4.60% | 0.41% | 31.54% | NA |
| VI/Aromatic | 96 | 16.70% | 82.30% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 35.60% | 17.80% | 1.11% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215734129 | G -> DEL | LOC_Os12g26850.1 | N | frameshift_variant | Average:7.091; most accessible tissue: Callus, score: 20.245 | N | N | N | N |
| vg1215734129 | G -> T | LOC_Os12g26850.1 | missense_variant ; p.Asn81Lys; MODERATE | nonsynonymous_codon | Average:7.091; most accessible tissue: Callus, score: 20.245 | benign  |
-0.458 |
DELETERIOUS | 0.03 |
| vg1215734129 | G -> T | LOC_Os12g26850.1 | missense_variant ; p.Asn81Lys; MODERATE | nonsynonymous_codon | Average:7.091; most accessible tissue: Callus, score: 20.245 | possibly damaging |
-1.918 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215734129 | NA | 3.06E-07 | mr1308 | 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 |
| vg1215734129 | NA | 6.34E-06 | mr1398 | 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 |
| vg1215734129 | NA | 1.87E-06 | mr1414 | 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 |
| vg1215734129 | 7.05E-06 | 8.67E-06 | mr1424 | 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 |
| vg1215734129 | 1.17E-06 | 1.17E-06 | mr1424 | 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 |
| vg1215734129 | NA | 4.34E-08 | mr1551 | 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 |
| vg1215734129 | NA | 5.31E-07 | mr1557 | 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 |
| vg1215734129 | NA | 4.79E-06 | mr1639 | 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 |
| vg1215734129 | NA | 1.32E-06 | mr1884 | 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 |