| Variant ID: vg0314622952 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14622952 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 241. )
AGAATAGCAATATTGTCCGTGCAATGGGATTTTAATTAAAAAAATCATGATTAACCCGTATATTATCTCTTAATTGCTATATAGCTCATTGTTTTTTCTC[A/G,T]
AAAAAAGTAGAGAGTTGGTAAGGAGTAATTAACATATGTGCCCTCTAGCCTGACTTATCCTTTTAGGTCTCGGAAAAAAATTAGGGAATTGGTATTGAAG
CTTCAATACCAATTCCCTAATTTTTTTCCGAGACCTAAAAGGATAAGTCAGGCTAGAGGGCACATATGTTAATTACTCCTTACCAACTCTCTACTTTTTT[T/C,A]
GAGAAAAAACAATGAGCTATATAGCAATTAAGAGATAATATACGGGTTAATCATGATTTTTTTAATTAAAATCCCATTGCACGGACAATATTGCTATTCT
| 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 | 87.20% | 10.50% | 2.20% | 0.00% | T: 0.06% |
| All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | T: 0.04% |
| All Japonica | 1512 | 60.80% | 32.50% | 6.61% | 0.00% | T: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.00% | 0.25% | 0.00% | T: 0.13% |
| Temperate Japonica | 767 | 27.50% | 60.90% | 11.60% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 1.60% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 89.60% | 7.10% | 2.90% | 0.00% | T: 0.41% |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 0.00% | T: 1.04% |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314622952 | A -> T | LOC_Os03g25570.1 | upstream_gene_variant ; 4461.0bp to feature; MODIFIER | silent_mutation | Average:64.794; most accessible tissue: Callus, score: 86.756 | N | N | N | N |
| vg0314622952 | A -> T | LOC_Os03g25560-LOC_Os03g25570 | intergenic_region ; MODIFIER | silent_mutation | Average:64.794; most accessible tissue: Callus, score: 86.756 | N | N | N | N |
| vg0314622952 | A -> G | LOC_Os03g25570.1 | upstream_gene_variant ; 4461.0bp to feature; MODIFIER | silent_mutation | Average:64.794; most accessible tissue: Callus, score: 86.756 | N | N | N | N |
| vg0314622952 | A -> G | LOC_Os03g25560-LOC_Os03g25570 | intergenic_region ; MODIFIER | silent_mutation | Average:64.794; most accessible tissue: Callus, score: 86.756 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314622952 | NA | 3.61E-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 |
| vg0314622952 | NA | 3.42E-17 | Spikelet_length | 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 |
| vg0314622952 | NA | 6.58E-13 | Spikelet_length | 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 |
| vg0314622952 | NA | 3.66E-06 | mr1044 | 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 |
| vg0314622952 | NA | 2.03E-08 | mr1045 | 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 |
| vg0314622952 | NA | 6.08E-07 | mr1045 | 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 |
| vg0314622952 | NA | 7.27E-06 | mr1063 | 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 |
| vg0314622952 | NA | 7.78E-28 | mr1115 | 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 |
| vg0314622952 | NA | 1.18E-34 | mr1137 | 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 |
| vg0314622952 | NA | 6.88E-11 | mr1137 | 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 |
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