| Variant ID: vg1221603903 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21603903 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 291. )
GGGCTAGGATTCGTCAGCTTCATATTGGTTTGTTATAAGATTTAAGTTGCCTTTATGGACAATGGTTTTTTCATAAAAACAGCTGGGGGTTAGGAGGAGT[A/T]
CCAAACTCTGTTTGCTGAGGGCAACTCTAGCGAGCGTACTCTTTTATTGTCACATGCAGATTTAATTTATTTTCAATTTTTCCATACATATTATGTCATG
CATGACATAATATGTATGGAAAAATTGAAAATAAATTAAATCTGCATGTGACAATAAAAGAGTACGCTCGCTAGAGTTGCCCTCAGCAAACAGAGTTTGG[T/A]
ACTCCTCCTAACCCCCAGCTGTTTTTATGAAAAAACCATTGTCCATAAAGGCAACTTAAATCTTATAACAAACCAATATGAAGCTGACGAATCCTAGCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.80% | 2.10% | 3.15% | 0.00% | NA |
| All Indica | 2759 | 94.70% | 0.50% | 4.75% | 0.00% | NA |
| All Japonica | 1512 | 93.50% | 5.40% | 1.12% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.60% | 1.00% | 11.43% | 0.00% | NA |
| Indica II | 465 | 95.30% | 0.40% | 4.30% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 94.00% | 0.80% | 5.22% | 0.00% | NA |
| Temperate Japonica | 767 | 90.90% | 7.60% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 9.10% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1221603903 | A -> T | LOC_Os12g35520.1 | upstream_gene_variant ; 3548.0bp to feature; MODIFIER | silent_mutation | Average:47.653; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1221603903 | A -> T | LOC_Os12g35540.1 | upstream_gene_variant ; 4906.0bp to feature; MODIFIER | silent_mutation | Average:47.653; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1221603903 | A -> T | LOC_Os12g35530.1 | downstream_gene_variant ; 829.0bp to feature; MODIFIER | silent_mutation | Average:47.653; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1221603903 | A -> T | LOC_Os12g35530-LOC_Os12g35540 | intergenic_region ; MODIFIER | silent_mutation | Average:47.653; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1221603903 | 1.35E-06 | 8.10E-07 | mr1222 | 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 |
| vg1221603903 | NA | 1.95E-06 | mr1305 | 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 |
| vg1221603903 | 1.85E-06 | 1.85E-06 | mr1370 | 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 |