| Variant ID: vg1216345816 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16345816 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.54, G: 0.46, others allele: 0.00, population size: 69. )
GTAAAATTTTAACTCATGAGTAAATCTGCGAGTAAAGTTTTTACTCGTGATGACGTGGACAAATCTCAGAGTCTATTTTTTTATCCAACAATAGTTTCCA[G/A,T]
GTTTCCACTACATGTATACATACGTAGTTTCCACCGTATATTTTCCCCTCTTTATCTTTTTATCCCACAAAATAGCATGACCTTTTTTTTAAACATTACT
AGTAATGTTTAAAAAAAAGGTCATGCTATTTTGTGGGATAAAAAGATAAAGAGGGGAAAATATACGGTGGAAACTACGTATGTATACATGTAGTGGAAAC[C/T,A]
TGGAAACTATTGTTGGATAAAAAAATAGACTCTGAGATTTGTCCACGTCATCACGAGTAAAAACTTTACTCGCAGATTTACTCATGAGTTAAAATTTTAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.30% | 38.30% | 0.17% | 2.18% | T: 0.08% |
| All Indica | 2759 | 52.20% | 46.60% | 0.18% | 0.91% | T: 0.14% |
| All Japonica | 1512 | 67.40% | 32.30% | 0.00% | 0.26% | NA |
| Aus | 269 | 88.80% | 1.10% | 0.37% | 9.67% | NA |
| Indica I | 595 | 27.20% | 72.30% | 0.50% | 0.00% | NA |
| Indica II | 465 | 65.40% | 32.70% | 0.43% | 1.51% | NA |
| Indica III | 913 | 60.70% | 38.30% | 0.00% | 0.99% | NA |
| Indica Intermediate | 786 | 53.30% | 45.00% | 0.00% | 1.15% | T: 0.51% |
| Temperate Japonica | 767 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 24.80% | 75.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.90% | 22.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 45.80% | 4.20% | 2.08% | 47.92% | NA |
| Intermediate | 90 | 66.70% | 31.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216345816 | G -> DEL | N | N | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> A | LOC_Os12g27710.1 | upstream_gene_variant ; 2991.0bp to feature; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> A | LOC_Os12g27720.1 | downstream_gene_variant ; 2767.0bp to feature; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> A | LOC_Os12g27710-LOC_Os12g27720 | intergenic_region ; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> T | LOC_Os12g27710.1 | upstream_gene_variant ; 2991.0bp to feature; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> T | LOC_Os12g27720.1 | downstream_gene_variant ; 2767.0bp to feature; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| vg1216345816 | G -> T | LOC_Os12g27710-LOC_Os12g27720 | intergenic_region ; MODIFIER | silent_mutation | Average:32.651; most accessible tissue: Callus, score: 72.966 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216345816 | 2.56E-06 | 2.56E-06 | mr1299 | Jap_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 |
| vg1216345816 | NA | 4.37E-06 | mr1345 | Jap_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 |
| vg1216345816 | NA | 2.43E-06 | mr1414 | Jap_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 |
| vg1216345816 | NA | 2.88E-08 | mr1551 | Jap_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 |
| vg1216345816 | NA | 6.06E-08 | mr1552 | Jap_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 |
| vg1216345816 | NA | 2.00E-06 | mr1639 | Jap_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 |
| vg1216345816 | NA | 4.79E-07 | mr1653 | Jap_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 |
| vg1216345816 | NA | 1.62E-07 | mr1682 | Jap_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 |
| vg1216345816 | NA | 1.70E-06 | mr1695 | Jap_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 |
| vg1216345816 | NA | 1.31E-07 | mr1700 | Jap_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 |
| vg1216345816 | 4.48E-06 | 4.48E-06 | mr1727 | Jap_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 |