| Variant ID: vg0100431870 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 431870 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 113. )
ACTTGCCTAGAAACCGCGAGACGAACCTTTTGAGCCTAGTTAATCTGTCATTAGCACATGTGAGTTACTGCAGCACTTATGACTAATCGTAGACTAATTA[A/G]
GCTCAAAAAAATTCGTCTCGTGATTTACATGCAAACTGTGCAATTAGTTTTTTCTTTTTGTCTATGTTTAATGCTCTATGCATGTGTTAAAAAATTCGAT
ATCGAATTTTTTAACACATGCATAGAGCATTAAACATAGACAAAAAGAAAAAACTAATTGCACAGTTTGCATGTAAATCACGAGACGAATTTTTTTGAGC[T/C]
TAATTAGTCTACGATTAGTCATAAGTGCTGCAGTAACTCACATGTGCTAATGACAGATTAACTAGGCTCAAAAGGTTCGTCTCGCGGTTTCTAGGCAAGT
| 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 | 72.30% | 0.40% | 5.59% | 21.73% | NA |
| All Indica | 2759 | 62.80% | 0.50% | 8.81% | 27.91% | NA |
| All Japonica | 1512 | 94.20% | 0.00% | 0.26% | 5.56% | NA |
| Aus | 269 | 39.00% | 1.90% | 4.83% | 54.28% | NA |
| Indica I | 595 | 52.30% | 1.00% | 24.54% | 22.18% | NA |
| Indica II | 465 | 87.30% | 0.40% | 0.86% | 11.40% | NA |
| Indica III | 913 | 54.40% | 0.10% | 4.49% | 40.96% | NA |
| Indica Intermediate | 786 | 66.00% | 0.50% | 6.62% | 26.84% | NA |
| Temperate Japonica | 767 | 88.70% | 0.00% | 0.52% | 10.82% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 1.04% | 16.67% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 3.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100431870 | A -> G | LOC_Os01g01800.1 | downstream_gene_variant ; 178.0bp to feature; MODIFIER | silent_mutation | Average:64.66; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
| vg0100431870 | A -> G | LOC_Os01g01810.1 | downstream_gene_variant ; 565.0bp to feature; MODIFIER | silent_mutation | Average:64.66; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
| vg0100431870 | A -> G | LOC_Os01g01800.2 | downstream_gene_variant ; 178.0bp to feature; MODIFIER | silent_mutation | Average:64.66; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
| vg0100431870 | A -> G | LOC_Os01g01800-LOC_Os01g01810 | intergenic_region ; MODIFIER | silent_mutation | Average:64.66; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
| vg0100431870 | A -> DEL | N | N | silent_mutation | Average:64.66; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100431870 | NA | 2.99E-07 | mr1870 | 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 |
| vg0100431870 | 9.63E-06 | 5.95E-11 | mr1582_2 | 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 |
| vg0100431870 | NA | 1.17E-08 | mr1870_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 |