| Variant ID: vg1216483033 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16483033 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGAACAACGGGTCAAGCGTCACCTTCTTCTACGCGTGGAGCACCGTGTTCAGGATGGATGTCGTCAGCATGACTGTCTCTAGATGCCGGTAGGAGGATTG[C/T]
AGTCAATTCATGGATGTTTCTAATTGGATGGATGTAGTGATGGTTTGATGGATTGATGAAGGATGATGTAAGTGTTGAGCTGAATTTAATTAAAGCTACT
AGTAGCTTTAATTAAATTCAGCTCAACACTTACATCATCCTTCATCAATCCATCAAACCATCACTACATCCATCCAATTAGAAACATCCATGAATTGACT[G/A]
CAATCCTCCTACCGGCATCTAGAGACAGTCATGCTGACGACATCCATCCTGAACACGGTGCTCCACGCGTAGAAGAAGGTGACGCTTGACCCGTTGTTCG
| 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 | 73.90% | 14.50% | 6.77% | 4.82% | NA |
| All Indica | 2759 | 69.10% | 21.30% | 6.89% | 2.65% | NA |
| All Japonica | 1512 | 80.00% | 3.40% | 7.41% | 9.26% | NA |
| Aus | 269 | 82.90% | 9.30% | 3.72% | 4.09% | NA |
| Indica I | 595 | 72.80% | 19.50% | 6.55% | 1.18% | NA |
| Indica II | 465 | 94.20% | 3.90% | 1.72% | 0.22% | NA |
| Indica III | 913 | 47.80% | 37.00% | 9.53% | 5.70% | NA |
| Indica Intermediate | 786 | 76.30% | 14.90% | 7.12% | 1.65% | NA |
| Temperate Japonica | 767 | 89.00% | 0.30% | 2.87% | 7.82% | NA |
| Tropical Japonica | 504 | 71.20% | 7.70% | 12.70% | 8.33% | NA |
| Japonica Intermediate | 241 | 69.30% | 4.10% | 10.79% | 15.77% | NA |
| VI/Aromatic | 96 | 85.40% | 11.50% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 78.90% | 11.10% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216483033 | C -> DEL | N | N | silent_mutation | Average:61.224; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg1216483033 | C -> T | LOC_Os12g27960.1 | upstream_gene_variant ; 3121.0bp to feature; MODIFIER | silent_mutation | Average:61.224; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg1216483033 | C -> T | LOC_Os12g27950.1 | downstream_gene_variant ; 9.0bp to feature; MODIFIER | silent_mutation | Average:61.224; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg1216483033 | C -> T | LOC_Os12g27950-LOC_Os12g27960 | intergenic_region ; MODIFIER | silent_mutation | Average:61.224; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216483033 | NA | 4.65E-06 | mr1532 | 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 |
| vg1216483033 | NA | 4.42E-06 | mr1648 | 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 |
| vg1216483033 | NA | 1.61E-06 | mr1796 | 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 |
| vg1216483033 | 2.03E-06 | 2.03E-06 | mr1966 | 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 |