| Variant ID: vg1220167325 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20167325 |
| 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: 59. )
CTGCGTCCGACTGGTTTCCAGTCGGGGGCTCTTGAGTTGTTGCCGTTTCAGTTGTTGCCGACTGGTTTCCAGTCGGCGGCAGGTCACTCGGATCGGCCCT[A/G]
TCGCCCGAAGCATGGGCACCAGTCGGCTGGCTTTCAGTGGTCGGCTGGTTTTCAACAGTCGGCTCGGGGTCCTTGGATATATTTTGCTCTGTCATGCCAG
CTGGCATGACAGAGCAAAATATATCCAAGGACCCCGAGCCGACTGTTGAAAACCAGCCGACCACTGAAAGCCAGCCGACTGGTGCCCATGCTTCGGGCGA[T/C]
AGGGCCGATCCGAGTGACCTGCCGCCGACTGGAAACCAGTCGGCAACAACTGAAACGGCAACAACTCAAGAGCCCCCGACTGGAAACCAGTCGGACGCAG
| 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 | 24.00% | 6.70% | 49.81% | 19.49% | NA |
| All Indica | 2759 | 3.70% | 10.10% | 69.74% | 16.46% | NA |
| All Japonica | 1512 | 64.30% | 1.10% | 14.09% | 20.57% | NA |
| Aus | 269 | 8.20% | 7.10% | 39.78% | 44.98% | NA |
| Indica I | 595 | 5.00% | 13.30% | 47.56% | 34.12% | NA |
| Indica II | 465 | 4.50% | 8.60% | 77.42% | 9.46% | NA |
| Indica III | 913 | 2.50% | 8.40% | 82.58% | 6.46% | NA |
| Indica Intermediate | 786 | 3.60% | 10.60% | 67.05% | 18.83% | NA |
| Temperate Japonica | 767 | 93.10% | 0.00% | 2.74% | 4.17% | NA |
| Tropical Japonica | 504 | 21.80% | 2.80% | 32.34% | 43.06% | NA |
| Japonica Intermediate | 241 | 61.40% | 0.80% | 12.03% | 25.73% | NA |
| VI/Aromatic | 96 | 5.20% | 2.10% | 67.71% | 25.00% | NA |
| Intermediate | 90 | 35.60% | 2.20% | 50.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220167325 | A -> DEL | LOC_Os12g33340.1 | N | frameshift_variant | Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| vg1220167325 | A -> G | LOC_Os12g33340.1 | synonymous_variant ; p.Asp438Asp; LOW | synonymous_codon | Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1220167325 | 4.07E-06 | 3.31E-07 | mr1224 | 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 |
| vg1220167325 | NA | 1.93E-08 | mr1593 | 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 |