| Variant ID: vg0430654505 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654505 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACTCCACAGGCATCCTCGACGGCACGGACGAAGCCTACTCCTCGGGGAAACCTTCATCTGACACATACCCGACCTCTGGGGTTGGGAAAAGTAGAGCAAG[A/G]
CTGAGTACTACCCACTGTACTCAGCAAGTCATACCGGAATAGGGGTATGATGCAGGGAATTAACAAAGAAGAGCTAGAGTGGTTCATTTGCATAAATACT
AGTATTTATGCAAATGAACCACTCTAGCTCTTCTTTGTTAATTCCCTGCATCATACCCCTATTCCGGTATGACTTGCTGAGTACAGTGGGTAGTACTCAG[T/C]
CTTGCTCTACTTTTCCCAACCCCAGAGGTCGGGTATGTGTCAGATGAAGGTTTCCCCGAGGAGTAGGCTTCGTCCGTGCCGTCGAGGATGCCTGTGGAGT
| 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 | 13.20% | 0.70% | 22.68% | 63.39% | NA |
| All Indica | 2759 | 1.40% | 1.20% | 33.13% | 64.30% | NA |
| All Japonica | 1512 | 37.50% | 0.10% | 0.46% | 61.97% | NA |
| Aus | 269 | 0.40% | 0.00% | 51.30% | 48.33% | NA |
| Indica I | 595 | 0.70% | 0.30% | 16.47% | 82.52% | NA |
| Indica II | 465 | 3.90% | 0.40% | 27.96% | 67.74% | NA |
| Indica III | 913 | 0.50% | 2.00% | 50.71% | 46.77% | NA |
| Indica Intermediate | 786 | 1.50% | 1.30% | 28.37% | 68.83% | NA |
| Temperate Japonica | 767 | 63.20% | 0.00% | 0.13% | 36.64% | NA |
| Tropical Japonica | 504 | 6.30% | 0.20% | 0.79% | 92.66% | NA |
| Japonica Intermediate | 241 | 20.70% | 0.00% | 0.83% | 78.42% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 11.11% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654505 | A -> DEL | N | N | silent_mutation | Average:5.261; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654505 | A -> G | LOC_Os04g51720.1 | downstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:5.261; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654505 | A -> G | LOC_Os04g51740.1 | downstream_gene_variant ; 2874.0bp to feature; MODIFIER | silent_mutation | Average:5.261; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0430654505 | A -> G | LOC_Os04g51730.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.261; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |