| Variant ID: vg1217862267 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17862267 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 236. )
AACCAAACCAGGAGATCAAGCCGTTGGTGACCGGTGAAGAATTTGGAATACAAGATTTTATTAATGACACCGGGCTAACTACGGATCAATTGCTACGAGG[C/T]
GCACCAATCGAAAAGGCGGAAGTGAAATACATGTACGAACTCGGTAAACCGTTTGTCAAGCCTGAGCAGCTGCAGTCCCTACCCGCACAAATGTACAAAT
ATTTGTACATTTGTGCGGGTAGGGACTGCAGCTGCTCAGGCTTGACAAACGGTTTACCGAGTTCGTACATGTATTTCACTTCCGCCTTTTCGATTGGTGC[G/A]
CCTCGTAGCAATTGATCCGTAGTTAGCCCGGTGTCATTAATAAAATCTTGTATTCCAAATTCTTCACCGGTCACCAACGGCTTGATCTCCTGGTTTGGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.70% | 7.30% | 1.27% | 27.66% | NA |
| All Indica | 2759 | 58.20% | 12.30% | 1.67% | 27.87% | NA |
| All Japonica | 1512 | 75.70% | 0.10% | 0.53% | 23.68% | NA |
| Aus | 269 | 55.80% | 0.00% | 0.00% | 44.24% | NA |
| Indica I | 595 | 63.50% | 29.10% | 0.67% | 6.72% | NA |
| Indica II | 465 | 48.00% | 10.30% | 3.66% | 38.06% | NA |
| Indica III | 913 | 55.30% | 3.40% | 1.53% | 39.76% | NA |
| Indica Intermediate | 786 | 63.50% | 11.10% | 1.40% | 24.05% | NA |
| Temperate Japonica | 767 | 97.90% | 0.10% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 47.60% | 0.20% | 0.99% | 51.19% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.00% | 0.83% | 35.68% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 2.08% | 46.88% | NA |
| Intermediate | 90 | 71.10% | 6.70% | 4.44% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217862267 | C -> DEL | N | N | silent_mutation | Average:13.995; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg1217862267 | C -> T | LOC_Os12g29874.1 | upstream_gene_variant ; 1888.0bp to feature; MODIFIER | silent_mutation | Average:13.995; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg1217862267 | C -> T | LOC_Os12g29860.1 | downstream_gene_variant ; 64.0bp to feature; MODIFIER | silent_mutation | Average:13.995; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg1217862267 | C -> T | LOC_Os12g29860-LOC_Os12g29874 | intergenic_region ; MODIFIER | silent_mutation | Average:13.995; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217862267 | 1.40E-07 | NA | mr1645 | 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 |
| vg1217862267 | 2.15E-06 | 1.90E-06 | mr1645 | 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 |
| vg1217862267 | 1.45E-06 | NA | mr1647 | 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 |
| vg1217862267 | NA | 6.78E-06 | mr1302_2 | 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 |