| Variant ID: vg1211898266 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11898266 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 236. )
TTTGTGTCTCTAAGCATCAGAAGAAGAAAACACAAAAGAGGTAAGCAAATGACAATACATTCTTTACTGAAGATACTAGCAGCATAATGCTATACGACTG[T/C]
TACTTATTTCAGTTTCTTGCAAGAACTACTAATGGAAGGATGTGCATCCAGTAAAAATAAACTCAATGGAGCAGACCATGAACATGATTACATGAATGGA
TCCATTCATGTAATCATGTTCATGGTCTGCTCCATTGAGTTTATTTTTACTGGATGCACATCCTTCCATTAGTAGTTCTTGCAAGAAACTGAAATAAGTA[A/G]
CAGTCGTATAGCATTATGCTGCTAGTATCTTCAGTAAAGAATGTATTGTCATTTGCTTACCTCTTTTGTGTTTTCTTCTTCTGATGCTTAGAGACACAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.50% | 0.20% | 3.36% | 5.88% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 70.80% | 0.50% | 10.32% | 18.39% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.00% | 0.00% | 1.69% | 7.30% | NA |
| Tropical Japonica | 504 | 40.50% | 1.40% | 25.20% | 32.94% | NA |
| Japonica Intermediate | 241 | 70.10% | 0.00% | 6.64% | 23.24% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211898266 | T -> C | LOC_Os12g20370.1 | upstream_gene_variant ; 3077.0bp to feature; MODIFIER | silent_mutation | Average:21.762; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| vg1211898266 | T -> C | LOC_Os12g20380.1 | upstream_gene_variant ; 2524.0bp to feature; MODIFIER | silent_mutation | Average:21.762; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| vg1211898266 | T -> C | LOC_Os12g20370-LOC_Os12g20380 | intergenic_region ; MODIFIER | silent_mutation | Average:21.762; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| vg1211898266 | T -> DEL | N | N | silent_mutation | Average:21.762; most accessible tissue: Zhenshan97 root, score: 38.035 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211898266 | NA | 5.68E-06 | mr1083 | 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 |
| vg1211898266 | 4.57E-06 | 4.57E-06 | mr1159_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 |
| vg1211898266 | 8.72E-06 | 8.72E-06 | mr1312_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 |
| vg1211898266 | 8.83E-06 | 8.83E-06 | mr1412_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 |
| vg1211898266 | NA | 5.97E-06 | mr1665_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 |
| vg1211898266 | 1.92E-06 | 3.54E-08 | mr1738_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 |
| vg1211898266 | NA | 1.92E-06 | mr1812_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 |
| vg1211898266 | 8.36E-06 | 8.36E-06 | mr1832_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 |
| vg1211898266 | 3.47E-06 | 3.47E-06 | mr1847_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 |