| Variant ID: vg0409586364 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586364 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACCCTATTCCTGCATGCAAATCGAAGAAACAAGCAAGAACAAGATAAAAGCAATCTGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTT[C/T]
CGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCGAGAAACCCTGAAGGGG
CCCCTTCAGGGTTTCTCGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCG[G/A]
AACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCAGATTGCTTTTATCTTGTTCTTGCTTGTTTCTTCGATTTGCATGCAGGAATAGGGTT
| 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 | 4.10% | 0.30% | 20.80% | 74.78% | NA |
| All Indica | 2759 | 6.10% | 0.00% | 27.33% | 66.58% | NA |
| All Japonica | 1512 | 0.90% | 0.80% | 10.05% | 88.29% | NA |
| Aus | 269 | 4.50% | 0.00% | 21.56% | 73.98% | NA |
| Indica I | 595 | 5.70% | 0.00% | 24.87% | 69.41% | NA |
| Indica II | 465 | 4.30% | 0.00% | 15.05% | 80.65% | NA |
| Indica III | 913 | 9.10% | 0.00% | 29.03% | 61.88% | NA |
| Indica Intermediate | 786 | 3.90% | 0.00% | 34.48% | 61.58% | NA |
| Temperate Japonica | 767 | 0.70% | 1.00% | 9.13% | 89.18% | NA |
| Tropical Japonica | 504 | 0.60% | 0.40% | 11.71% | 87.30% | NA |
| Japonica Intermediate | 241 | 2.10% | 0.80% | 9.54% | 87.55% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 16.67% | 82.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586364 | C -> DEL | N | N | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586364 | C -> T | LOC_Os04g17510.1 | upstream_gene_variant ; 1673.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586364 | C -> T | LOC_Os04g17530.1 | downstream_gene_variant ; 1874.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586364 | C -> T | LOC_Os04g17540.1 | downstream_gene_variant ; 4333.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586364 | C -> T | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |