| Variant ID: vg0631247242 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 31247242 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )
ATCAATGACCGGAAGCGAGAACGCTGTGGCTACAACCCTGGACGACTCCATGTCGAAGGATCCTCCCGCAGAAGTGGAGAACGGAACGTCGACGACATCC[G/A]
AGCCCGAGAAGGATCCTAGTGCACCCAAATCTTATCCTTCCGACGAGAATCACGGGCCGACAAGAACAACTTCCGAGGCCACAAGGTCCCGATGTCCTAT
ATAGGACATCGGGACCTTGTGGCCTCGGAAGTTGTTCTTGTCGGCCCGTGATTCTCGTCGGAAGGATAAGATTTGGGTGCACTAGGATCCTTCTCGGGCT[C/T]
GGATGTCGTCGACGTTCCGTTCTCCACTTCTGCGGGAGGATCCTTCGACATGGAGTCGTCCAGGGTTGTAGCCACAGCGTTCTCGCTTCCGGTCATTGAT
| 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 | 73.40% | 17.20% | 8.51% | 0.85% | NA |
| All Indica | 2759 | 61.60% | 25.70% | 12.00% | 0.69% | NA |
| All Japonica | 1512 | 91.90% | 5.20% | 1.85% | 0.99% | NA |
| Aus | 269 | 84.80% | 1.10% | 12.64% | 1.49% | NA |
| Indica I | 595 | 69.60% | 16.50% | 12.94% | 1.01% | NA |
| Indica II | 465 | 75.10% | 17.00% | 7.31% | 0.65% | NA |
| Indica III | 913 | 45.00% | 42.30% | 12.05% | 0.66% | NA |
| Indica Intermediate | 786 | 66.80% | 18.70% | 13.99% | 0.51% | NA |
| Temperate Japonica | 767 | 96.90% | 1.60% | 1.04% | 0.52% | NA |
| Tropical Japonica | 504 | 83.90% | 10.90% | 3.37% | 1.79% | NA |
| Japonica Intermediate | 241 | 92.90% | 5.00% | 1.24% | 0.83% | NA |
| VI/Aromatic | 96 | 86.50% | 9.40% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 76.70% | 15.60% | 6.67% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0631247242 | G -> A | LOC_Os06g51570.1 | upstream_gene_variant ; 3636.0bp to feature; MODIFIER | silent_mutation | Average:20.398; most accessible tissue: Callus, score: 57.402 | N | N | N | N |
| vg0631247242 | G -> DEL | N | N | silent_mutation | Average:20.398; most accessible tissue: Callus, score: 57.402 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0631247242 | 2.42E-06 | 5.85E-07 | mr1489 | 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 |
| vg0631247242 | 1.96E-06 | NA | mr1758 | 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 |