| Variant ID: vg1211548501 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11548501 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCCGGCCCAAATCAGCCAACACCCCAGCCGAGCCGCCTCCTCCTCCCGTGCGCGTGTTGCGCACGGCGCACGCCGCCGCAAACGTCGCCGCTAAGGAAA[C/T,G]
GAAGTCGGCGCCGTCATTCTTTTCTTCACGTCGCCGCAGCCGTGCCTTCGTTGCCCTCCTCCTCTGCGAACCGACCTTCGAAGCCTATAAATACCGGCGA
TCGCCGGTATTTATAGGCTTCGAAGGTCGGTTCGCAGAGGAGGAGGGCAACGAAGGCACGGCTGCGGCGACGTGAAGAAAAGAATGACGGCGCCGACTTC[G/A,C]
TTTCCTTAGCGGCGACGTTTGCGGCGGCGTGCGCCGTGCGCAACACGCGCACGGGAGGAGGAGGCGGCTCGGCTGGGGTGTTGGCTGATTTGGGCCGGCT
| 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 | 46.10% | 0.70% | 1.46% | 51.65% | G: 0.06% |
| All Indica | 2759 | 49.10% | 0.00% | 0.83% | 50.02% | G: 0.04% |
| All Japonica | 1512 | 47.90% | 2.20% | 2.84% | 47.02% | NA |
| Aus | 269 | 10.80% | 0.00% | 0.74% | 88.48% | NA |
| Indica I | 595 | 51.60% | 0.00% | 0.34% | 48.07% | NA |
| Indica II | 465 | 45.40% | 0.00% | 0.43% | 54.19% | NA |
| Indica III | 913 | 51.40% | 0.00% | 1.31% | 47.32% | NA |
| Indica Intermediate | 786 | 46.80% | 0.00% | 0.89% | 52.16% | G: 0.13% |
| Temperate Japonica | 767 | 79.70% | 3.40% | 4.17% | 12.78% | NA |
| Tropical Japonica | 504 | 9.70% | 0.00% | 1.39% | 88.89% | NA |
| Japonica Intermediate | 241 | 27.00% | 2.90% | 1.66% | 68.46% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 0.00% | 76.04% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 1.11% | 43.33% | G: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211548501 | C -> DEL | N | N | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> G | LOC_Os12g19800.1 | upstream_gene_variant ; 1451.0bp to feature; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> G | LOC_Os12g19810.1 | downstream_gene_variant ; 3437.0bp to feature; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> G | LOC_Os12g19800-LOC_Os12g19810 | intergenic_region ; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> T | LOC_Os12g19800.1 | upstream_gene_variant ; 1451.0bp to feature; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> T | LOC_Os12g19810.1 | downstream_gene_variant ; 3437.0bp to feature; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| vg1211548501 | C -> T | LOC_Os12g19800-LOC_Os12g19810 | intergenic_region ; MODIFIER | silent_mutation | Average:16.208; most accessible tissue: Callus, score: 36.516 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211548501 | 2.64E-08 | 2.64E-08 | mr1024_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 |
| vg1211548501 | NA | 6.44E-06 | mr1565_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 |
| vg1211548501 | NA | 2.47E-06 | mr1913_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 |