| Variant ID: vg0136579622 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36579622 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 30. )
CACAGTTGAAACAGGACCCCGGTTTTGTGCCAGTCTCCTTCTTGGCTTGCGCGGACGGGGCTGGCTGTGCTGGTGCCATTGGTGGGCGTGGAGCTGCACC[A/G]
CGGTTGGGCTGGCCTCCCTGGTGGTTCGGACTGCCGCTAGCGCCCTGGTGGAAGTTGCTAGAGTGGAACGGGCGGTGCTGACGGACGATCATGGTGGTAG
CTACCACCATGATCGTCCGTCAGCACCGCCCGTTCCACTCTAGCAACTTCCACCAGGGCGCTAGCGGCAGTCCGAACCACCAGGGAGGCCAGCCCAACCG[T/C]
GGTGCAGCTCCACGCCCACCAATGGCACCAGCACAGCCAGCCCCGTCCGCGCAAGCCAAGAAGGAGACTGGCACAAAACCGGGGTCCTGTTTCAACTGTG
| 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 | 36.50% | 15.40% | 1.76% | 46.32% | NA |
| All Indica | 2759 | 6.00% | 17.50% | 2.54% | 73.98% | NA |
| All Japonica | 1512 | 98.00% | 0.50% | 0.00% | 1.52% | NA |
| Aus | 269 | 1.10% | 85.10% | 2.23% | 11.52% | NA |
| Indica I | 595 | 7.70% | 5.90% | 5.38% | 81.01% | NA |
| Indica II | 465 | 7.10% | 39.40% | 2.15% | 51.40% | NA |
| Indica III | 913 | 1.80% | 10.20% | 0.88% | 87.19% | NA |
| Indica Intermediate | 786 | 8.90% | 21.90% | 2.54% | 66.67% | NA |
| Temperate Japonica | 767 | 98.80% | 0.30% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 97.20% | 0.80% | 0.00% | 1.98% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 25.00% | 4.20% | 2.08% | 68.75% | NA |
| Intermediate | 90 | 57.80% | 5.60% | 5.56% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136579622 | A -> G | LOC_Os01g63120.1 | synonymous_variant ; p.Arg325Arg; LOW | synonymous_codon | Average:12.476; most accessible tissue: Callus, score: 21.6 | N | N | N | N |
| vg0136579622 | A -> DEL | LOC_Os01g63120.1 | N | frameshift_variant | Average:12.476; most accessible tissue: Callus, score: 21.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136579622 | NA | 1.44E-08 | mr1193 | 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 |
| vg0136579622 | NA | 1.59E-06 | mr1291 | 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 |
| vg0136579622 | NA | 2.99E-06 | mr1543 | 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 |
| vg0136579622 | NA | 9.07E-06 | mr1660 | 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 |
| vg0136579622 | NA | 8.73E-06 | mr1684 | 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 |
| vg0136579622 | NA | 3.88E-09 | mr1722 | 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 |