| Variant ID: vg1222420005 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22420005 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 68. )
TGCTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAATACTTTAAAT[A/G]
TGTTTCTGTATACTTAAAAAAGATTTGGCACACGAACTAAACACAGCCTAAATAAAGTGCTCAAGAATATACATGAGATTATATTCACAACATTGCCCAT
ATGGGCAATGTTGTGAATATAATCTCATGTATATTCTTGAGCACTTTATTTAGGCTGTGTTTAGTTCGTGTGCCAAATCTTTTTTAAGTATACAGAAACA[T/C]
ATTTAAAGTATTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.20% | 19.70% | 1.42% | 55.71% | NA |
| All Indica | 2759 | 2.30% | 14.70% | 2.17% | 80.83% | NA |
| All Japonica | 1512 | 64.70% | 21.60% | 0.33% | 13.29% | NA |
| Aus | 269 | 1.50% | 33.80% | 0.74% | 63.94% | NA |
| Indica I | 595 | 2.20% | 21.30% | 2.52% | 73.95% | NA |
| Indica II | 465 | 3.70% | 1.70% | 2.80% | 91.83% | NA |
| Indica III | 913 | 1.80% | 14.20% | 1.10% | 82.91% | NA |
| Indica Intermediate | 786 | 2.20% | 17.90% | 2.80% | 77.10% | NA |
| Temperate Japonica | 767 | 71.80% | 19.60% | 0.00% | 8.60% | NA |
| Tropical Japonica | 504 | 65.30% | 11.90% | 0.79% | 22.02% | NA |
| Japonica Intermediate | 241 | 41.10% | 48.50% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 8.30% | 87.50% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 45.60% | 25.60% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420005 | A -> DEL | N | N | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420005 | A -> G | LOC_Os12g36600.1 | downstream_gene_variant ; 4389.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420005 | A -> G | LOC_Os12g36610.1 | downstream_gene_variant ; 740.0bp to feature; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| vg1222420005 | A -> G | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.11; most accessible tissue: Callus, score: 63.722 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222420005 | NA | 4.85E-07 | mr1180 | 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 |
| vg1222420005 | NA | 9.59E-08 | mr1183 | 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 |
| vg1222420005 | NA | 5.95E-07 | mr1503 | 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 |
| vg1222420005 | NA | 1.44E-06 | mr1227_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 |
| vg1222420005 | NA | 2.01E-07 | mr1921_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 |