| Variant ID: vg1224168671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 24168671 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )
ATATTTCTCTCGGTGGATCGAGGCCGAACCCCTCGGAGCAATCACTTCGGCAACAGTACAGAAGTTTGTTAGGAAAAACATAATCTGCCGTTTCGGAGTG[C/G]
CAAAAGAGTTCATCACTGACAATGGCAAGCAGTTCGACTCTGACAAGTTCAGAGAGATGTGCGAAGGACTTAACCTGCAAATCAGGTTCGCGTCGGTCGC
GCGACCGACGCGAACCTGATTTGCAGGTTAAGTCCTTCGCACATCTCTCTGAACTTGTCAGAGTCGAACTGCTTGCCATTGTCAGTGATGAACTCTTTTG[G/C]
CACTCCGAAACGGCAGATTATGTTTTTCCTAACAAACTTCTGTACTGTTGCCGAAGTGATTGCTCCGAGGGGTTCGGCCTCGATCCACCGAGAGAAATAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.30% | 13.10% | 3.58% | 0.00% | NA |
| All Indica | 2759 | 76.70% | 17.80% | 5.51% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.20% | 0.00% | NA |
| Aus | 269 | 50.90% | 45.40% | 3.72% | 0.00% | NA |
| Indica I | 595 | 82.90% | 12.80% | 4.37% | 0.00% | NA |
| Indica II | 465 | 81.10% | 12.90% | 6.02% | 0.00% | NA |
| Indica III | 913 | 75.00% | 19.30% | 5.70% | 0.00% | NA |
| Indica Intermediate | 786 | 71.40% | 22.80% | 5.85% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1224168671 | C -> G | LOC_Os12g39260.1 | downstream_gene_variant ; 285.0bp to feature; MODIFIER | silent_mutation | Average:45.631; most accessible tissue: Minghui63 flag leaf, score: 84.028 | N | N | N | N |
| vg1224168671 | C -> G | LOC_Os12g39270.1 | downstream_gene_variant ; 275.0bp to feature; MODIFIER | silent_mutation | Average:45.631; most accessible tissue: Minghui63 flag leaf, score: 84.028 | N | N | N | N |
| vg1224168671 | C -> G | LOC_Os12g39260-LOC_Os12g39270 | intergenic_region ; MODIFIER | silent_mutation | Average:45.631; most accessible tissue: Minghui63 flag leaf, score: 84.028 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1224168671 | 1.27E-06 | NA | mr1004 | 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 |
| vg1224168671 | 3.02E-06 | NA | mr1005 | 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 |
| vg1224168671 | NA | 4.15E-06 | mr1005 | 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 |
| vg1224168671 | 6.60E-06 | 1.50E-07 | mr1011 | 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 |
| vg1224168671 | 3.23E-07 | 3.22E-07 | mr1012 | 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 |