| Variant ID: vg0413108547 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13108547 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 107. )
GCATTTTTCTTGGTTATTCGTCTGGTGTGAAAGGCTATAAGTTATGGTGTCCTGAAACCAAAAAGGTTGTGATTAGTAGAAATGTTGTCTTCCATGAATC[G/A]
GTTATGTTACATGACAAACCTTCTACTAATGTTCCTGTTGAGAGTCAGGAGAAAGCAAGTGTGCAGGTGGAGCACTTGATCAGTTCAGGGCATGCACCAG
CTGGTGCATGCCCTGAACTGATCAAGTGCTCCACCTGCACACTTGCTTTCTCCTGACTCTCAACAGGAACATTAGTAGAAGGTTTGTCATGTAACATAAC[C/T]
GATTCATGGAAGACAACATTTCTACTAATCACAACCTTTTTGGTTTCAGGACACCATAACTTATAGCCTTTCACACCAGACGAATAACCAAGAAAAATGC
| 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 | 44.60% | 14.50% | 3.68% | 37.20% | NA |
| All Indica | 2759 | 16.70% | 24.60% | 5.62% | 53.10% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.07% | 0.79% | NA |
| Aus | 269 | 4.80% | 0.70% | 5.58% | 88.85% | NA |
| Indica I | 595 | 30.80% | 44.90% | 1.85% | 22.52% | NA |
| Indica II | 465 | 11.60% | 22.60% | 5.38% | 60.43% | NA |
| Indica III | 913 | 11.30% | 18.70% | 7.67% | 62.32% | NA |
| Indica Intermediate | 786 | 15.30% | 17.30% | 6.23% | 61.20% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 56.70% | 5.60% | 3.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0413108547 | G -> DEL | LOC_Os04g23070.1 | N | frameshift_variant | Average:5.591; most accessible tissue: Callus, score: 12.873 | N | N | N | N |
| vg0413108547 | G -> A | LOC_Os04g23070.1 | synonymous_variant ; p.Ser526Ser; LOW | synonymous_codon | Average:5.591; most accessible tissue: Callus, score: 12.873 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413108547 | NA | 5.94E-06 | mr1215 | 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 |
| vg0413108547 | NA | 1.33E-06 | mr1461 | 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 |
| vg0413108547 | 4.09E-06 | NA | mr1746 | 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 |