| Variant ID: vg1218161124 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18161124 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )
CAGCCGTTGCAAGCTCATGCCCATCCCGCGTTTGATTATGAGGGGGCCTCTGACAAGACACGGATATCGTCGCGGGGTACTCGTTCTCACATTGCCATCC[C/T]
TCTTATTGCCGATGACAATATTTTTAAGCTTTATATCTAATTCTTCCTCGACTTTTCGTTGTGTTGCAGCTCTTCGCACGGATATCGTGACGCAGCGGGT
ACCCGCTGCGTCACGATATCCGTGCGAAGAGCTGCAACACAACGAAAAGTCGAGGAAGAATTAGATATAAAGCTTAAAAATATTGTCATCGGCAATAAGA[G/A]
GGATGGCAATGTGAGAACGAGTACCCCGCGACGATATCCGTGTCTTGTCAGAGGCCCCCTCATAATCAAACGCGGGATGGGCATGAGCTTGCAACGGCTG
| 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 | 70.90% | 4.30% | 1.93% | 22.79% | NA |
| All Indica | 2759 | 58.60% | 2.90% | 3.26% | 35.16% | NA |
| All Japonica | 1512 | 94.90% | 4.80% | 0.00% | 0.33% | NA |
| Aus | 269 | 56.90% | 10.80% | 0.37% | 31.97% | NA |
| Indica I | 595 | 79.50% | 6.40% | 6.72% | 7.39% | NA |
| Indica II | 465 | 51.00% | 2.40% | 2.37% | 44.30% | NA |
| Indica III | 913 | 50.10% | 1.80% | 1.97% | 46.22% | NA |
| Indica Intermediate | 786 | 57.40% | 2.00% | 2.67% | 37.91% | NA |
| Temperate Japonica | 767 | 99.20% | 0.30% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.80% | 20.70% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 78.10% | 14.60% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 80.00% | 10.00% | 0.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218161124 | C -> DEL | N | N | silent_mutation | Average:46.716; most accessible tissue: Zhenshan97 young leaf, score: 74.675 | N | N | N | N |
| vg1218161124 | C -> T | LOC_Os12g30280.1 | downstream_gene_variant ; 3837.0bp to feature; MODIFIER | silent_mutation | Average:46.716; most accessible tissue: Zhenshan97 young leaf, score: 74.675 | N | N | N | N |
| vg1218161124 | C -> T | LOC_Os12g30270.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.716; most accessible tissue: Zhenshan97 young leaf, score: 74.675 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218161124 | 3.42E-06 | NA | mr1064 | 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 |
| vg1218161124 | 8.02E-06 | NA | mr1534 | 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 |
| vg1218161124 | 7.71E-06 | NA | mr1745 | 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 |
| vg1218161124 | 6.53E-06 | 4.02E-06 | mr1758 | 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 |
| vg1218161124 | NA | 6.52E-06 | mr1528_2 | 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 |