| Variant ID: vg0315011446 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 15011446 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
TGTGGCTGCTGCAGACGCGCGACGCCGTCTTCGACGCCGAGGACGCCCTCGATCATTTCTATCTCCGCGTCGATATGTCCAGGTATATATAGCTGCTACT[A/AT]
GATACTCCCTCTATTTTTTAATAGACGACGCCGTTGACTTTTTCTTCCATATTTGACTATTCGTCTTATTCAAAAAATTTTATGTAAATATATAAAATAT
ATATTTTATATATTTACATAAAATTTTTTGAATAAGACGAATAGTCAAATATGGAAGAAAAAGTCAACGGCGTCGTCTATTAAAAAATAGAGGGAGTATC[T/AT]
AGTAGCAGCTATATATACCTGGACATATCGACGCGGAGATAGAAATGATCGAGGGCGTCCTCGGCGTCGAAGACGGCGTCGCGCGTCTGCAGCAGCCACA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011446 | A -> AT | LOC_Os03g26240.1 | upstream_gene_variant ; 1994.0bp to feature; MODIFIER | silent_mutation | Average:62.065; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011446 | A -> AT | LOC_Os03g26260.1 | upstream_gene_variant ; 4359.0bp to feature; MODIFIER | silent_mutation | Average:62.065; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011446 | A -> AT | LOC_Os03g26229.1 | downstream_gene_variant ; 3187.0bp to feature; MODIFIER | silent_mutation | Average:62.065; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011446 | A -> AT | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.065; most accessible tissue: Callus, score: 78.971 | N | N | N | N |