| Variant ID: vg1223942507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23942507 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )
AATGAAAAAAACCAAGAAATCAAATTCAAAATTAAGTTCTAAAATTTAATTTTGGGTTATAAGCATAAGCATAAGCCAAACAATTAGCCCTTTTTTCACC[A/G]
GAGGGCGCACTTTTTATATATGAGTCGTCGAATGAAGGATTCTTTTTTTGGAGCATTATGTGTTGTGTTCTAGTGCAAACTCATATACCGACTCATGATA
TATCATGAGTCGGTATATGAGTTTGCACTAGAACACAACACATAATGCTCCAAAAAAAGAATCCTTCATTCGACGACTCATATATAAAAAGTGCGCCCTC[T/C]
GGTGAAAAAAGGGCTAATTGTTTGGCTTATGCTTATGCTTATAACCCAAAATTAAATTTTAGAACTTAATTTTGAATTTGATTTCTTGGTTTTTTTCATT
| 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 | 83.70% | 10.00% | 3.36% | 3.00% | NA |
| All Indica | 2759 | 94.20% | 0.50% | 0.18% | 5.07% | NA |
| All Japonica | 1512 | 61.50% | 29.30% | 9.13% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.00% | 0.50% | 0.17% | NA |
| Indica II | 465 | 79.40% | 1.30% | 0.22% | 19.14% | NA |
| Indica III | 913 | 99.50% | 0.20% | 0.00% | 0.33% | NA |
| Indica Intermediate | 786 | 93.00% | 0.90% | 0.13% | 5.98% | NA |
| Temperate Japonica | 767 | 38.30% | 49.40% | 12.13% | 0.13% | NA |
| Tropical Japonica | 504 | 89.30% | 5.80% | 4.96% | 0.00% | NA |
| Japonica Intermediate | 241 | 77.20% | 14.50% | 8.30% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 14.40% | 13.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223942507 | A -> DEL | N | N | silent_mutation | Average:59.25; most accessible tissue: Callus, score: 80.224 | N | N | N | N |
| vg1223942507 | A -> G | LOC_Os12g38930.1 | upstream_gene_variant ; 1084.0bp to feature; MODIFIER | silent_mutation | Average:59.25; most accessible tissue: Callus, score: 80.224 | N | N | N | N |
| vg1223942507 | A -> G | LOC_Os12g38940.1 | downstream_gene_variant ; 1610.0bp to feature; MODIFIER | silent_mutation | Average:59.25; most accessible tissue: Callus, score: 80.224 | N | N | N | N |
| vg1223942507 | A -> G | LOC_Os12g38930-LOC_Os12g38940 | intergenic_region ; MODIFIER | silent_mutation | Average:59.25; most accessible tissue: Callus, score: 80.224 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1223942507 | NA | 1.83E-12 | Plant_height | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1223942507 | NA | 4.26E-08 | mr1137_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 |
| vg1223942507 | NA | 7.77E-08 | mr1748_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 |
| vg1223942507 | 1.51E-09 | NA | mr1768_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 |
| vg1223942507 | NA | 2.03E-06 | mr1768_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 |