| Variant ID: vg0315011173 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011173 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGTATAAGCAAATTAAAGATTGTCTGCAGAAAGGAAAACTCAAACAAATCAATTAGAGAGAGAGAGAGAGAGAGTAAATCGATCGACAATGGCGGAGGC[G/A]
ATCATCGGGCCGCTGGTGTGGAGGCTGCAGGAGATGGCGGTGGGGCAGGCTCGGGCGCTGGTGTCGGTGAACGACGACATCGTGAGGCTCCGGGACAGGC
GCCTGTCCCGGAGCCTCACGATGTCGTCGTTCACCGACACCAGCGCCCGAGCCTGCCCCACCGCCATCTCCTGCAGCCTCCACACCAGCGGCCCGATGAT[C/T]
GCCTCCGCCATTGTCGATCGATTTACTCTCTCTCTCTCTCTCTCTAATTGATTTGTTTGAGTTTTCCTTTCTGCAGACAATCTTTAATTTGCTTATACAT
| 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 | 99.60% | 0.30% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.50% | 0.14% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.38% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011173 | G -> A | LOC_Os03g26250.1 | synonymous_variant ; p.Ala4Ala; LOW | N | Average:66.62; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |
| vg0315011173 | G -> A | LOC_Os03g26240.1 | upstream_gene_variant ; 1720.0bp to feature; MODIFIER | N | Average:66.62; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |
| vg0315011173 | G -> A | LOC_Os03g26260.1 | upstream_gene_variant ; 4633.0bp to feature; MODIFIER | N | Average:66.62; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |
| vg0315011173 | G -> A | LOC_Os03g26229.1 | downstream_gene_variant ; 2913.0bp to feature; MODIFIER | N | Average:66.62; most accessible tissue: Minghui63 root, score: 82.511 | N | N | N | N |