| Variant ID: vg1218540256 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18540256 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTAATTACTCGGATAGCAAAAGGGCTAGGGGTCGTTAGCGACCAAATTGCTTTTATCTCAGCCGCTCGTCCGTGTATCGATGAGACTTATCTAGTGCAAG[G/A]
GCATATTTTGAAACATGGAGTATATGGATCTTTGATATACTTTTTCCCCGGTTGTACAAATGAAATCCCGTTGCCAAATGCGGGGTATCATTTGTACAAC
GTTGTACAAATGATACCCCGCATTTGGCAACGGGATTTCATTTGTACAACCGGGGAAAAAGTATATCAAAGATCCATATACTCCATGTTTCAAAATATGC[C/T]
CTTGCACTAGATAAGTCTCATCGATACACGGACGAGCGGCTGAGATAAAAGCAATTTGGTCGCTAACGACCCCTAGCCCTTTTGCTATCCGAGTAATTAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.90% | 0.40% | 3.32% | 80.32% | NA |
| All Indica | 2759 | 5.70% | 0.80% | 4.46% | 89.09% | NA |
| All Japonica | 1512 | 36.70% | 0.00% | 0.00% | 63.29% | NA |
| Aus | 269 | 4.80% | 0.00% | 9.29% | 85.87% | NA |
| Indica I | 595 | 9.40% | 0.50% | 4.54% | 85.55% | NA |
| Indica II | 465 | 6.20% | 0.60% | 1.29% | 91.83% | NA |
| Indica III | 913 | 1.90% | 1.20% | 6.68% | 90.25% | NA |
| Indica Intermediate | 786 | 7.00% | 0.50% | 3.69% | 88.80% | NA |
| Temperate Japonica | 767 | 61.90% | 0.00% | 0.00% | 38.07% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 0.00% | 95.24% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 0.00% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 6.25% | 93.75% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 3.33% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218540256 | G -> DEL | N | N | silent_mutation | Average:12.731; most accessible tissue: Callus, score: 30.037 | N | N | N | N |
| vg1218540256 | G -> A | LOC_Os12g30850.1 | downstream_gene_variant ; 2415.0bp to feature; MODIFIER | silent_mutation | Average:12.731; most accessible tissue: Callus, score: 30.037 | N | N | N | N |
| vg1218540256 | G -> A | LOC_Os12g30850-LOC_Os12g30880 | intergenic_region ; MODIFIER | silent_mutation | Average:12.731; most accessible tissue: Callus, score: 30.037 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218540256 | NA | 3.87E-07 | mr1236_2 | 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 |
| vg1218540256 | NA | 1.19E-07 | mr1236_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 |
| vg1218540256 | NA | 8.84E-06 | mr1421_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 |
| vg1218540256 | NA | 3.77E-06 | mr1428_2 | 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 |
| vg1218540256 | NA | 1.53E-06 | mr1954_2 | 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 |
| vg1218540256 | NA | 3.52E-06 | mr1954_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 |