| Variant ID: vg1203644489 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 3644489 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, A: 0.21, others allele: 0.00, population size: 82. )
TGAAGCAGCGCAGCCAACAAGAAGAAGCAATAGCAGCATTTAGTCGTGTGAAATCAAGGCGATATATTTGATTGTTTATATGGCTTATTGATAAAAAAAA[C/A]
CCCCAAGGATTAAGCCATTAAGGGCCTGCATGGGAGTATATTTGTAATTCTTTTCCGGTTGCTTTAAGATTGGTGGGATGGGCTGAAAAGGCTTGAAAAC
GTTTTCAAGCCTTTTCAGCCCATCCCACCAATCTTAAAGCAACCGGAAAAGAATTACAAATATACTCCCATGCAGGCCCTTAATGGCTTAATCCTTGGGG[G/T]
TTTTTTTTATCAATAAGCCATATAAACAATCAAATATATCGCCTTGATTTCACACGACTAAATGCTGCTATTGCTTCTTCTTGTTGGCTGCGCTGCTTCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.60% | 36.70% | 1.44% | 11.24% | NA |
| All Indica | 2759 | 84.20% | 5.10% | 1.49% | 9.17% | NA |
| All Japonica | 1512 | 1.30% | 93.80% | 1.39% | 3.51% | NA |
| Aus | 269 | 3.70% | 13.00% | 1.86% | 81.41% | NA |
| Indica I | 595 | 90.10% | 2.90% | 0.00% | 7.06% | NA |
| Indica II | 465 | 73.80% | 2.60% | 1.29% | 22.37% | NA |
| Indica III | 913 | 89.30% | 6.70% | 2.19% | 1.86% | NA |
| Indica Intermediate | 786 | 80.20% | 6.50% | 1.91% | 11.45% | NA |
| Temperate Japonica | 767 | 1.30% | 98.40% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 90.10% | 0.40% | 8.33% | NA |
| Japonica Intermediate | 241 | 1.70% | 86.70% | 7.05% | 4.56% | NA |
| VI/Aromatic | 96 | 10.40% | 88.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 31.10% | 62.20% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1203644489 | C -> DEL | N | N | silent_mutation | Average:53.377; most accessible tissue: Callus, score: 94.239 | N | N | N | N |
| vg1203644489 | C -> A | LOC_Os12g07390.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.377; most accessible tissue: Callus, score: 94.239 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1203644489 | NA | 5.22E-07 | mr1411 | 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 |
| vg1203644489 | NA | 4.51E-06 | mr1835 | 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 |
| vg1203644489 | NA | 9.30E-18 | mr1131_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 |
| vg1203644489 | NA | 8.25E-20 | mr1199_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 |
| vg1203644489 | NA | 4.01E-07 | mr1925_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 |