| Variant ID: vg0206427310 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6427310 |
| 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: 313. )
ATCCTCTTGATCTTCATCTGGCTGAATAATGAGCACATATGCACAGGACACAAATACATTCAGTCAGCCCTTGAGTTATCACTTCCAAGACATCATTTGC[A/G]
TGCTTATATTAGGAAGCCTGGAGACTCACCTCAGGTAGCTTTGTTTCAGGAATTCGCTCTTGAAATTGGACGCTAGGTGCATGTTGAAGTTTTGAAAGAT
ATCTTTCAAAACTTCAACATGCACCTAGCGTCCAATTTCAAGAGCGAATTCCTGAAACAAAGCTACCTGAGGTGAGTCTCCAGGCTTCCTAATATAAGCA[T/C]
GCAAATGATGTCTTGGAAGTGATAACTCAAGGGCTGACTGAATGTATTTGTGTCCTGTGCATATGTGCTCATTATTCAGCCAGATGAAGATCAAGAGGAT
| 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 | 97.00% | 1.50% | 1.21% | 0.30% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 90.80% | 4.70% | 3.57% | 0.93% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 4.17% | 0.00% | NA |
| Tropical Japonica | 504 | 80.60% | 13.70% | 3.37% | 2.38% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.80% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0206427310 | A -> G | LOC_Os02g12340.1 | upstream_gene_variant ; 3306.0bp to feature; MODIFIER | silent_mutation | Average:52.29; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| vg0206427310 | A -> G | LOC_Os02g12350.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.29; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| vg0206427310 | A -> DEL | N | N | silent_mutation | Average:52.29; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206427310 | 8.74E-09 | 1.01E-07 | mr1188 | Jap_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 |
| vg0206427310 | NA | 1.79E-06 | mr1543 | 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 |
| vg0206427310 | NA | 3.60E-07 | mr1188_2 | 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 |