| Variant ID: vg1217852416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17852416 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.05, others allele: 0.00, population size: 177. )
TTCTGGAGCTTCGGCAGACGATTGACGATCTCTTCTTCTTCGCAAAGCTGACCATCTAGTACTAGTTGAAATTCGAAGAAGGAAGAAGGAAGTAAACCTT[T/C]
TGCAAATAGCATTAGGGAAAGGAGGAAAAAGGAACTTTCGCAAATATTTTCATTTATAAAATATGTCCTTACGTTTTATCCAGTTGGCTTATCCTACAGT
ACTGTAGGATAAGCCAACTGGATAAAACGTAAGGACATATTTTATAAATGAAAATATTTGCGAAAGTTCCTTTTTCCTCCTTTCCCTAATGCTATTTGCA[A/G]
AAGGTTTACTTCCTTCTTCCTTCTTCGAATTTCAACTAGTACTAGATGGTCAGCTTTGCGAAGAAGAAGAGATCGTCAATCGTCTGCCGAAGCTCCAGAA
| 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 | 51.30% | 12.30% | 1.69% | 34.68% | NA |
| All Indica | 2759 | 37.50% | 19.70% | 2.28% | 40.49% | NA |
| All Japonica | 1512 | 75.10% | 0.40% | 0.73% | 23.81% | NA |
| Aus | 269 | 45.70% | 7.40% | 2.23% | 44.61% | NA |
| Indica I | 595 | 49.20% | 9.40% | 2.52% | 38.82% | NA |
| Indica II | 465 | 44.70% | 10.50% | 1.94% | 42.80% | NA |
| Indica III | 913 | 24.30% | 27.30% | 2.63% | 45.78% | NA |
| Indica Intermediate | 786 | 39.80% | 24.00% | 1.91% | 34.22% | NA |
| Temperate Japonica | 767 | 97.80% | 0.10% | 0.13% | 1.96% | NA |
| Tropical Japonica | 504 | 47.20% | 0.40% | 1.39% | 50.99% | NA |
| Japonica Intermediate | 241 | 61.00% | 1.20% | 1.24% | 36.51% | NA |
| VI/Aromatic | 96 | 72.90% | 2.10% | 0.00% | 25.00% | NA |
| Intermediate | 90 | 68.90% | 11.10% | 0.00% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217852416 | T -> C | LOC_Os12g29860.1 | upstream_gene_variant ; 2516.0bp to feature; MODIFIER | silent_mutation | Average:6.402; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1217852416 | T -> C | LOC_Os12g29850.1 | downstream_gene_variant ; 42.0bp to feature; MODIFIER | silent_mutation | Average:6.402; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1217852416 | T -> C | LOC_Os12g29850-LOC_Os12g29860 | intergenic_region ; MODIFIER | silent_mutation | Average:6.402; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1217852416 | T -> DEL | N | N | silent_mutation | Average:6.402; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217852416 | 8.45E-06 | 8.45E-06 | mr1321 | Ind_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 |
| vg1217852416 | 9.37E-07 | 9.37E-07 | mr1323 | Ind_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 |
| vg1217852416 | NA | 3.73E-06 | mr1732 | Ind_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 |
| vg1217852416 | 5.08E-06 | NA | mr1979 | 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 |