| Variant ID: vg0306598441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6598441 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTTTTATGGGTTGCTTTCCATGAGGCTGACTAAACTGAACAAGCAATTCGGAGCATGGATTCTGTGCAAGCTAGACCCATCATCAGGTAATCTGTTTGC[G/A]
GGATCTAGACATGAAATTTGTTTGACATGTGAGGATGTCAGCCTACTTTTGGGAATCCCTTGTGGACGGAAGGAGATTTTGCCTGCAATAAAAAACGAGG
CCTCGTTTTTTATTGCAGGCAAAATCTCCTTCCGTCCACAAGGGATTCCCAAAAGTAGGCTGACATCCTCACATGTCAAACAAATTTCATGTCTAGATCC[C/T]
GCAAACAGATTACCTGATGATGGGTCTAGCTTGCACAGAATCCATGCTCCGAATTGCTTGTTCAGTTTAGTCAGCCTCATGGAAAGCAACCCATAAAACT
| 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 | 32.70% | 0.10% | 18.62% | 48.54% | NA |
| All Indica | 2759 | 1.50% | 0.00% | 26.24% | 72.27% | NA |
| All Japonica | 1512 | 95.80% | 0.50% | 0.33% | 3.37% | NA |
| Aus | 269 | 0.70% | 0.00% | 24.16% | 75.09% | NA |
| Indica I | 595 | 1.50% | 0.00% | 25.21% | 73.28% | NA |
| Indica II | 465 | 1.90% | 0.00% | 19.57% | 78.49% | NA |
| Indica III | 913 | 1.00% | 0.00% | 34.83% | 64.18% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 20.99% | 77.23% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 94.20% | 0.00% | 0.20% | 5.56% | NA |
| Japonica Intermediate | 241 | 95.00% | 2.90% | 1.24% | 0.83% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 70.83% | 18.75% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 20.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306598441 | G -> A | LOC_Os03g12470.1 | downstream_gene_variant ; 4404.0bp to feature; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598441 | G -> A | LOC_Os03g12490.1 | downstream_gene_variant ; 3722.0bp to feature; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598441 | G -> A | LOC_Os03g12480.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |
| vg0306598441 | G -> DEL | N | N | silent_mutation | Average:4.917; most accessible tissue: Callus, score: 9.417 | N | N | N | N |