| Variant ID: vg1126074837 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26074837 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 68. )
AGTTGACAGAGTGACAGAGTGGAAGCAGTTCAAGCAGTTGAAGTTTCGCTGATGTCTAAATATAATTAGCAGGTTGAAGCAAAGTGTAAGAACATTTAAG[G/C]
CTTAGTTATTTACAGATTACTAGCAATGTACCCGTGTGTTGCAATAGGAAATATAATTCGTTTACAATATAGAACGAGCTCTTCTACCGGCGAATCGATG
CATCGATTCGCCGGTAGAAGAGCTCGTTCTATATTGTAAACGAATTATATTTCCTATTGCAACACACGGGTACATTGCTAGTAATCTGTAAATAACTAAG[C/G]
CTTAAATGTTCTTACACTTTGCTTCAACCTGCTAATTATATTTAGACATCAGCGAAACTTCAACTGCTTGAACTGCTTCCACTCTGTCACTCTGTCAACT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.10% | 10.40% | 7.60% | 1.88% | NA |
| All Indica | 2759 | 81.50% | 9.90% | 7.97% | 0.58% | NA |
| All Japonica | 1512 | 76.50% | 11.20% | 7.67% | 4.56% | NA |
| Aus | 269 | 78.80% | 14.50% | 6.32% | 0.37% | NA |
| Indica I | 595 | 80.50% | 7.60% | 11.26% | 0.67% | NA |
| Indica II | 465 | 74.00% | 17.00% | 8.17% | 0.86% | NA |
| Indica III | 913 | 87.30% | 7.70% | 4.60% | 0.44% | NA |
| Indica Intermediate | 786 | 80.00% | 10.20% | 9.29% | 0.51% | NA |
| Temperate Japonica | 767 | 96.30% | 1.40% | 1.30% | 0.91% | NA |
| Tropical Japonica | 504 | 41.50% | 29.40% | 18.06% | 11.11% | NA |
| Japonica Intermediate | 241 | 86.70% | 4.60% | 6.22% | 2.49% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 7.80% | 6.67% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126074837 | G -> DEL | N | N | silent_mutation | Average:39.008; most accessible tissue: Minghui63 root, score: 70.332 | N | N | N | N |
| vg1126074837 | G -> C | LOC_Os11g43220.1 | downstream_gene_variant ; 87.0bp to feature; MODIFIER | silent_mutation | Average:39.008; most accessible tissue: Minghui63 root, score: 70.332 | N | N | N | N |
| vg1126074837 | G -> C | LOC_Os11g43230.1 | downstream_gene_variant ; 3016.0bp to feature; MODIFIER | silent_mutation | Average:39.008; most accessible tissue: Minghui63 root, score: 70.332 | N | N | N | N |
| vg1126074837 | G -> C | LOC_Os11g43220-LOC_Os11g43230 | intergenic_region ; MODIFIER | silent_mutation | Average:39.008; most accessible tissue: Minghui63 root, score: 70.332 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126074837 | 4.01E-07 | NA | mr1644 | 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 |
| vg1126074837 | 7.04E-08 | 2.11E-06 | mr1644 | 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 |
| vg1126074837 | 4.37E-06 | NA | mr1191_2 | 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 |
| vg1126074837 | 4.22E-06 | NA | mr1238_2 | 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 |