| Variant ID: vg0430654546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654546 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCGGGGAAACCTTCATCTGACACATACCCGACCTCTGGGGTTGGGAAAAGTAGAGCAAGACTGAGTACTACCCACTGTACTCAGCAAGTCATACCGGAAT[A/G]
GGGGTATGATGCAGGGAATTAACAAAGAAGAGCTAGAGTGGTTCATTTGCATAAATACTGGCATTTATAAACAGGAATTTAATGCGAAAACAGTTGTAAT
ATTACAACTGTTTTCGCATTAAATTCCTGTTTATAAATGCCAGTATTTATGCAAATGAACCACTCTAGCTCTTCTTTGTTAATTCCCTGCATCATACCCC[T/C]
ATTCCGGTATGACTTGCTGAGTACAGTGGGTAGTACTCAGTCTTGCTCTACTTTTCCCAACCCCAGAGGTCGGGTATGTGTCAGATGAAGGTTTCCCCGA
| 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 | 13.30% | 0.60% | 27.74% | 58.29% | NA |
| All Indica | 2759 | 1.60% | 1.10% | 41.10% | 56.29% | NA |
| All Japonica | 1512 | 37.60% | 0.10% | 1.59% | 60.78% | NA |
| Aus | 269 | 0.40% | 0.00% | 45.35% | 54.28% | NA |
| Indica I | 595 | 0.50% | 0.30% | 19.83% | 79.33% | NA |
| Indica II | 465 | 3.90% | 0.40% | 33.76% | 61.94% | NA |
| Indica III | 913 | 1.20% | 1.90% | 62.98% | 33.95% | NA |
| Indica Intermediate | 786 | 1.40% | 1.00% | 36.13% | 61.45% | NA |
| Temperate Japonica | 767 | 63.10% | 0.00% | 0.13% | 36.77% | NA |
| Tropical Japonica | 504 | 6.50% | 0.20% | 3.57% | 89.68% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.00% | 2.07% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 15.62% | 84.38% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 17.78% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654546 | A -> DEL | N | N | silent_mutation | Average:5.654; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654546 | A -> G | LOC_Os04g51720.1 | downstream_gene_variant ; 2148.0bp to feature; MODIFIER | silent_mutation | Average:5.654; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654546 | A -> G | LOC_Os04g51740.1 | downstream_gene_variant ; 2833.0bp to feature; MODIFIER | silent_mutation | Average:5.654; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654546 | A -> G | LOC_Os04g51730.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.654; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |