| Variant ID: vg1204011153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4011153 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GACCCAGTCTTCGTCCTGCGTGTCCTCAACGTGTCGCTTACGTGGCATTAGAGTAAAAAAAATTGTGGGACCAACATATCATTCACACACAAAAAAAAAT[A/G]
GTGGAACCCACCGACATGGGGCCCACATTTCATCCTCACCTCTCCCCCTCTCTCTCTCATTTTTGTCTCTCTTACATTCCATCAGCCGGCCGAAACACGA
TCGTGTTTCGGCCGGCTGATGGAATGTAAGAGAGACAAAAATGAGAGAGAGAGGGGGAGAGGTGAGGATGAAATGTGGGCCCCATGTCGGTGGGTTCCAC[T/C]
ATTTTTTTTTGTGTGTGAATGATATGTTGGTCCCACAATTTTTTTTACTCTAATGCCACGTAAGCGACACGTTGAGGACACGCAGGACGAAGACTGGGTC
| 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 | 27.60% | 6.60% | 0.23% | 65.59% | NA |
| All Indica | 2759 | 7.10% | 0.50% | 0.25% | 92.10% | NA |
| All Japonica | 1512 | 62.80% | 19.10% | 0.07% | 18.06% | NA |
| Aus | 269 | 10.40% | 0.00% | 0.74% | 88.85% | NA |
| Indica I | 595 | 1.70% | 0.20% | 0.67% | 97.48% | NA |
| Indica II | 465 | 17.60% | 0.90% | 0.22% | 81.29% | NA |
| Indica III | 913 | 4.80% | 0.10% | 0.00% | 95.07% | NA |
| Indica Intermediate | 786 | 7.80% | 1.00% | 0.25% | 90.97% | NA |
| Temperate Japonica | 767 | 83.60% | 11.70% | 0.13% | 4.56% | NA |
| Tropical Japonica | 504 | 42.10% | 26.40% | 0.00% | 31.55% | NA |
| Japonica Intermediate | 241 | 39.80% | 27.40% | 0.00% | 32.78% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 0.00% | 14.58% | NA |
| Intermediate | 90 | 54.40% | 7.80% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204011153 | A -> DEL | N | N | silent_mutation | Average:18.947; most accessible tissue: Callus, score: 69.366 | N | N | N | N |
| vg1204011153 | A -> G | LOC_Os12g07900.1 | upstream_gene_variant ; 362.0bp to feature; MODIFIER | silent_mutation | Average:18.947; most accessible tissue: Callus, score: 69.366 | N | N | N | N |
| vg1204011153 | A -> G | LOC_Os12g07910.1 | upstream_gene_variant ; 1131.0bp to feature; MODIFIER | silent_mutation | Average:18.947; most accessible tissue: Callus, score: 69.366 | N | N | N | N |
| vg1204011153 | A -> G | LOC_Os12g07900-LOC_Os12g07910 | intergenic_region ; MODIFIER | silent_mutation | Average:18.947; most accessible tissue: Callus, score: 69.366 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204011153 | NA | 1.81E-06 | mr1345 | 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 |
| vg1204011153 | 6.12E-06 | NA | mr1653 | 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 |
| vg1204011153 | NA | 5.36E-06 | mr1653 | 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 |