| Variant ID: vg1216532803 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16532803 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 128. )
GCTATATTAACTGTCGGGATCAGGAATGAGATTCCCAACCTGTCACTCTAAAGATTTAATTACAATTAATACAACGATATAATCGGATCGTAGATTGGAC[A/C]
ATTAGTTTTGGAGAAAAATCGTTTCGAAGCTCGCTAAAATGCATGCATGTATGAGGTGGAGAGAGAGAGGAGAGAGTAGTGATACGAAGTTTCACGAATT
AATTCGTGAAACTTCGTATCACTACTCTCTCCTCTCTCTCTCCACCTCATACATGCATGCATTTTAGCGAGCTTCGAAACGATTTTTCTCCAAAACTAAT[T/G]
GTCCAATCTACGATCCGATTATATCGTTGTATTAATTGTAATTAAATCTTTAGAGTGACAGGTTGGGAATCTCATTCCTGATCCCGACAGTTAATATAGC
| 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 | 92.00% | 4.80% | 0.83% | 2.33% | NA |
| All Indica | 2759 | 86.80% | 7.90% | 1.38% | 3.88% | NA |
| All Japonica | 1512 | 99.50% | 0.30% | 0.00% | 0.20% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 1.80% | 0.00% | 0.67% | NA |
| Indica II | 465 | 64.10% | 20.20% | 3.66% | 12.04% | NA |
| Indica III | 913 | 93.00% | 4.60% | 0.77% | 1.64% | NA |
| Indica Intermediate | 786 | 85.10% | 9.00% | 1.78% | 4.07% | NA |
| Temperate Japonica | 767 | 99.50% | 0.30% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1216532803 | A -> C | LOC_Os12g28020.1 | downstream_gene_variant ; 2257.0bp to feature; MODIFIER | silent_mutation | Average:43.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1216532803 | A -> C | LOC_Os12g28040.1 | downstream_gene_variant ; 4752.0bp to feature; MODIFIER | silent_mutation | Average:43.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1216532803 | A -> C | LOC_Os12g28020-LOC_Os12g28040 | intergenic_region ; MODIFIER | silent_mutation | Average:43.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1216532803 | A -> DEL | N | N | silent_mutation | Average:43.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216532803 | NA | 3.48E-06 | mr1425 | 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 |
| vg1216532803 | NA | 1.04E-06 | mr1425 | 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 |
| vg1216532803 | 1.51E-06 | 2.44E-08 | mr1829 | Ind_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 |
| vg1216532803 | NA | 1.56E-06 | mr1842 | 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 |