| Variant ID: vg0318751093 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18751093 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )
TGTGGTGGGAAATGGCTTCGAACTTGTTCAAGGTTGCACGGCCGAAGATGGCGTTGTAGTTGTACGGGATGTCGACAACGTCGAACAATACTTGCTCTTC[G/A]
CGTCTGTTTTCCGCCGTGCGGAAGGCTACCATCAACTGTGCTTGGCCAAGAACTTGAACTGCTTCTCCGCTGAAACGTCGGAGCGATGCTGGTGCTGGGG
CCCCAGCACCAGCATCGCTCCGACGTTTCAGCGGAGAAGCAGTTCAAGTTCTTGGCCAAGCACAGTTGATGGTAGCCTTCCGCACGGCGGAAAACAGACG[C/T]
GAAGAGCAAGTATTGTTCGACGTTGTCGACATCCCGTACAACTACAACGCCATCTTCGGCCGTGCAACCTTGAACAAGTTCGAAGCCATTTCCCACCACA
| 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 | 93.90% | 0.80% | 5.04% | 0.34% | NA |
| All Indica | 2759 | 89.60% | 1.30% | 8.52% | 0.58% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 65.70% | 4.20% | 28.24% | 1.85% | NA |
| Indica II | 465 | 96.60% | 0.40% | 2.80% | 0.22% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 91.60% | 1.10% | 6.74% | 0.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318751093 | G -> A | LOC_Os03g32749.1 | synonymous_variant ; p.Arg682Arg; LOW | synonymous_codon | Average:52.47; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| vg0318751093 | G -> DEL | LOC_Os03g32749.1 | N | frameshift_variant | Average:52.47; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318751093 | NA | 9.36E-08 | Spikelet_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0318751093 | 4.59E-06 | NA | mr1864 | 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 |