| Variant ID: vg0409586287 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586287 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACCGTACGAGACGTTGTGTTGCGCCTTAGCGATCGATACACCTCTCCGTGGGTTGCTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCATGCAAATC[G/A]
AAGAAACAAGCAAGAACAAGATAAAAGCAATCTGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGT
ACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCAGATTGCTTTTATCTTGTTCTTGCTTGTTTCTT[C/T]
GATTTGCATGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAGCAACCCACGGAGAGGTGTATCGATCGCTAAGGCGCAACACAACGTCTCGTACGGTT
| 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 | 24.70% | 0.30% | 21.98% | 53.05% | NA |
| All Indica | 2759 | 7.10% | 0.00% | 20.15% | 72.71% | NA |
| All Japonica | 1512 | 60.50% | 0.70% | 19.51% | 19.25% | NA |
| Aus | 269 | 9.30% | 0.00% | 30.86% | 59.85% | NA |
| Indica I | 595 | 8.40% | 0.00% | 15.46% | 76.13% | NA |
| Indica II | 465 | 5.40% | 0.00% | 14.19% | 80.43% | NA |
| Indica III | 913 | 8.20% | 0.00% | 23.00% | 68.78% | NA |
| Indica Intermediate | 786 | 6.00% | 0.00% | 23.92% | 70.10% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 1.04% | 2.87% | NA |
| Tropical Japonica | 504 | 5.60% | 1.40% | 48.21% | 44.84% | NA |
| Japonica Intermediate | 241 | 62.20% | 1.70% | 18.26% | 17.84% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 75.00% | 15.62% | NA |
| Intermediate | 90 | 24.40% | 1.10% | 36.67% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586287 | G -> DEL | N | N | silent_mutation | Average:5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0409586287 | G -> A | LOC_Os04g17510.1 | upstream_gene_variant ; 1596.0bp to feature; MODIFIER | silent_mutation | Average:5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0409586287 | G -> A | LOC_Os04g17530.1 | downstream_gene_variant ; 1951.0bp to feature; MODIFIER | silent_mutation | Average:5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0409586287 | G -> A | LOC_Os04g17540.1 | downstream_gene_variant ; 4410.0bp to feature; MODIFIER | silent_mutation | Average:5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0409586287 | G -> A | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.266; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |