| Variant ID: vg1216386926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16386926 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTAATGAACAAGTGGACCCAATGTATCTTGTTTTCGAAAGGAAGTCCATCAAAAGCTCTAGCAATGTGAGGGTTGGCAACCAAATGAGCATAGTAAACA[G/A]
ATACATGGATCTCCTCAAACCCAGGAAGGCTTTTCAAGGTTTGAAATAAACCATCTGGCAGTTTATTGTCTGGCTCAGCGACCTTTAGTATAGCAGAAGC
GCTTCTGCTATACTAAAGGTCGCTGAGCCAGACAATAAACTGCCAGATGGTTTATTTCAAACCTTGAAAAGCCTTCCTGGGTTTGAGGAGATCCATGTAT[C/T]
TGTTTACTATGCTCATTTGGTTGCCAACCCTCACATTGCTAGAGCTTTTGATGGACTTCCTTTCGAAAACAAGATACATTGGGTCCACTTGTTCATTAAT
| 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 | 98.90% | 0.00% | 0.49% | 0.55% | NA |
| All Indica | 2759 | 98.40% | 0.00% | 0.83% | 0.72% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.00% | 2.18% | 0.34% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.22% | 0.22% | NA |
| Indica III | 913 | 98.60% | 0.00% | 0.44% | 0.99% | NA |
| Indica Intermediate | 786 | 98.30% | 0.00% | 0.64% | 1.02% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1216386926 | G -> A | LOC_Os12g27800.1 | missense_variant ; p.Ser541Phe; MODERATE | N | Average:11.643; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216386926 | G -> A | LOC_Os12g27810.1 | upstream_gene_variant ; 4499.0bp to feature; MODIFIER | N | Average:11.643; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216386926 | G -> A | LOC_Os12g27790.1 | downstream_gene_variant ; 2904.0bp to feature; MODIFIER | N | Average:11.643; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |