| Variant ID: vg1214515514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14515514 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )
TCAGGCCAGAAGCATGTTAGTTATGCCAGCAGTAGAACTGACGGGGAAGTAGTCAAGAGTTAGTAAGATCAGGAGCTAAATGAGAATTTCTTTATGAGGA[G/A]
TTTCCTATCAACAACTGAGGGTTAAGTTCCAAGTCTTGTCCTGGATGAAAGTGCATCGTCATTGCTTTATTTTGATTGATCGATGAAGTTTTCTATTTTC
GAAAATAGAAAACTTCATCGATCAATCAAAATAAAGCAATGACGATGCACTTTCATCCAGGACAAGACTTGGAACTTAACCCTCAGTTGTTGATAGGAAA[C/T]
TCCTCATAAAGAAATTCTCATTTAGCTCCTGATCTTACTAACTCTTGACTACTTCCCCGTCAGTTCTACTGCTGGCATAACTAACATGCTTCTGGCCTGA
| 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 | 59.40% | 4.00% | 16.12% | 20.48% | NA |
| All Indica | 2759 | 40.20% | 6.30% | 25.41% | 28.09% | NA |
| All Japonica | 1512 | 92.30% | 0.30% | 0.73% | 6.75% | NA |
| Aus | 269 | 53.20% | 2.20% | 14.87% | 29.74% | NA |
| Indica I | 595 | 67.40% | 1.70% | 22.69% | 8.24% | NA |
| Indica II | 465 | 40.00% | 11.00% | 20.43% | 28.60% | NA |
| Indica III | 913 | 21.80% | 8.50% | 29.68% | 39.98% | NA |
| Indica Intermediate | 786 | 41.00% | 4.60% | 25.45% | 29.01% | NA |
| Temperate Japonica | 767 | 90.50% | 0.30% | 0.52% | 8.74% | NA |
| Tropical Japonica | 504 | 96.80% | 0.20% | 0.40% | 2.58% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.40% | 2.07% | 9.13% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 77.80% | 1.10% | 10.00% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214515514 | G -> DEL | N | N | silent_mutation | Average:33.875; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| vg1214515514 | G -> A | LOC_Os12g25240.1 | upstream_gene_variant ; 1785.0bp to feature; MODIFIER | silent_mutation | Average:33.875; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| vg1214515514 | G -> A | LOC_Os12g25250.1 | upstream_gene_variant ; 3852.0bp to feature; MODIFIER | silent_mutation | Average:33.875; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| vg1214515514 | G -> A | LOC_Os12g25230.1 | downstream_gene_variant ; 1164.0bp to feature; MODIFIER | silent_mutation | Average:33.875; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| vg1214515514 | G -> A | LOC_Os12g25230-LOC_Os12g25240 | intergenic_region ; MODIFIER | silent_mutation | Average:33.875; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214515514 | 4.75E-06 | NA | mr1264 | 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 |
| vg1214515514 | 8.47E-06 | NA | mr1264 | 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 |
| vg1214515514 | 2.26E-06 | NA | mr1655 | 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 |