| Variant ID: vg0401291884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1291884 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGAATCTGGATGTCATTCTTGGAATGAACTGGTTGACGAAGCATAGTGGTATTATAGATTGTGCTAGCCGATCCATATCTTTGATTGGGGGTACTGGCCA[A/G]
CGAGTCATTTTCCATGCTAAGCCTGCACTTCCTTGTAAGCAAGTTCTGAACCAGGTCAGTATGGAGGAAATACCCATCGTGAAAGAGTATCCAGATGTTT
AAACATCTGGATACTCTTTCACGATGGGTATTTCCTCCATACTGACCTGGTTCAGAACTTGCTTACAAGGAAGTGCAGGCTTAGCATGGAAAATGACTCG[T/C]
TGGCCAGTACCCCCAATCAAAGATATGGATCGGCTAGCACAATCTATAATACCACTATGCTTCGTCAACCAGTTCATTCCAAGAATGACATCCAGATTCT
| 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 | 42.30% | 6.80% | 4.08% | 46.87% | NA |
| All Indica | 2759 | 36.80% | 7.10% | 3.44% | 52.70% | NA |
| All Japonica | 1512 | 55.20% | 1.10% | 0.46% | 43.32% | NA |
| Aus | 269 | 34.20% | 33.50% | 31.60% | 0.74% | NA |
| Indica I | 595 | 70.90% | 0.00% | 2.18% | 26.89% | NA |
| Indica II | 465 | 25.40% | 3.40% | 1.51% | 69.68% | NA |
| Indica III | 913 | 19.30% | 13.70% | 5.48% | 61.56% | NA |
| Indica Intermediate | 786 | 37.90% | 7.00% | 3.18% | 51.91% | NA |
| Temperate Japonica | 767 | 55.40% | 1.30% | 0.39% | 42.89% | NA |
| Tropical Japonica | 504 | 66.30% | 0.20% | 0.20% | 33.33% | NA |
| Japonica Intermediate | 241 | 31.10% | 2.10% | 1.24% | 65.56% | NA |
| VI/Aromatic | 96 | 11.50% | 11.50% | 4.17% | 72.92% | NA |
| Intermediate | 90 | 51.10% | 8.90% | 2.22% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401291884 | A -> DEL | LOC_Os04g03110.1 | N | frameshift_variant | Average:13.237; most accessible tissue: Callus, score: 39.017 | N | N | N | N |
| vg0401291884 | A -> G | LOC_Os04g03110.1 | synonymous_variant ; p.Gln448Gln; LOW | synonymous_codon | Average:13.237; most accessible tissue: Callus, score: 39.017 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401291884 | 2.78E-07 | NA | mr1757 | 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 |
| vg0401291884 | 1.79E-08 | NA | mr1549_2 | 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 |
| vg0401291884 | 1.63E-08 | NA | mr1757_2 | 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 |