| Variant ID: vg0409586370 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586370 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTCCTGCATGCAAATCGAAGAAACAAGCAAGAACAAGATAAAAGCAATCTGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAG[A/T]
ACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCGAGAAACCCTGAAGGGGTAACTA
TAGTTACCCCTTCAGGGTTTCTCGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGT[T/A]
CTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCAGATTGCTTTTATCTTGTTCTTGCTTGTTTCTTCGATTTGCATGCAGGAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.50% | 0.20% | 15.13% | 82.16% | NA |
| All Indica | 2759 | 3.60% | 0.00% | 18.74% | 77.71% | NA |
| All Japonica | 1512 | 0.90% | 0.60% | 11.84% | 86.71% | NA |
| Aus | 269 | 1.50% | 0.00% | 1.49% | 97.03% | NA |
| Indica I | 595 | 4.00% | 0.00% | 15.80% | 80.17% | NA |
| Indica II | 465 | 3.40% | 0.00% | 12.04% | 84.52% | NA |
| Indica III | 913 | 4.50% | 0.00% | 18.29% | 77.22% | NA |
| Indica Intermediate | 786 | 2.20% | 0.00% | 25.45% | 72.39% | NA |
| Temperate Japonica | 767 | 0.80% | 0.80% | 9.13% | 89.31% | NA |
| Tropical Japonica | 504 | 0.40% | 0.20% | 15.87% | 83.53% | NA |
| Japonica Intermediate | 241 | 2.10% | 0.80% | 12.03% | 85.06% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 4.17% | 93.75% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 12.22% | 85.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586370 | A -> DEL | N | N | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586370 | A -> T | LOC_Os04g17510.1 | upstream_gene_variant ; 1679.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586370 | A -> T | LOC_Os04g17530.1 | downstream_gene_variant ; 1868.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586370 | A -> T | LOC_Os04g17540.1 | downstream_gene_variant ; 4327.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586370 | A -> T | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |