| Variant ID: vg0409586319 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586319 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCGATACACCTCTCCGTGGGTTGCTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCATGCAAATCGAAGAAACAAGCAAGAACAAGATAAAAGCAAT[C/T]
TGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCA
TGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCA[G/A]
ATTGCTTTTATCTTGTTCTTGCTTGTTTCTTCGATTTGCATGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAGCAACCCACGGAGAGGTGTATCGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.00% | 0.40% | 23.49% | 49.09% | NA |
| All Indica | 2759 | 10.30% | 0.80% | 24.97% | 63.97% | NA |
| All Japonica | 1512 | 58.70% | 0.00% | 15.28% | 25.99% | NA |
| Aus | 269 | 13.40% | 0.00% | 46.84% | 39.78% | NA |
| Indica I | 595 | 12.30% | 0.80% | 19.33% | 67.56% | NA |
| Indica II | 465 | 6.70% | 0.60% | 15.05% | 77.63% | NA |
| Indica III | 913 | 11.80% | 0.90% | 26.40% | 60.90% | NA |
| Indica Intermediate | 786 | 9.20% | 0.60% | 33.46% | 56.74% | NA |
| Temperate Japonica | 767 | 83.30% | 0.00% | 12.39% | 4.30% | NA |
| Tropical Japonica | 504 | 16.10% | 0.00% | 21.63% | 62.30% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 11.20% | 19.09% | NA |
| VI/Aromatic | 96 | 40.60% | 0.00% | 36.46% | 22.92% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 32.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586319 | C -> DEL | N | N | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586319 | C -> T | LOC_Os04g17510.1 | upstream_gene_variant ; 1628.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586319 | C -> T | LOC_Os04g17530.1 | downstream_gene_variant ; 1919.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586319 | C -> T | LOC_Os04g17540.1 | downstream_gene_variant ; 4378.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586319 | C -> T | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |