| Variant ID: vg1000477694 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 477694 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACAACACGGCTAGGTGGAGTTAGCACCCTTCTGGTGTCTATCCATTCTCTGTATTGACATCTCCTTGGTGGTTCCTGGGAGAAAAGAATAGATGTGAAGC[G/A]
AGCAAAGTTAGTAAATGTTGTGAGAAAATAAGGATTCATGATAATCAAAATATTCTTACCATGAAATCGTTGTCGAGAATATTTGAACAAACAAAGAACC
GGTTCTTTGTTTGTTCAAATATTCTCGACAACGATTTCATGGTAAGAATATTTTGATTATCATGAATCCTTATTTTCTCACAACATTTACTAACTTTGCT[C/T]
GCTTCACATCTATTCTTTTCTCCCAGGAACCACCAAGGAGATGTCAATACAGAGAATGGATAGACACCAGAAGGGTGCTAACTCCACCTAGCCGTGTTGT
| 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 | 92.60% | 0.10% | 2.05% | 5.27% | NA |
| All Indica | 2759 | 96.30% | 0.00% | 0.54% | 3.12% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.20% | 0.33% | NA |
| Aus | 269 | 28.60% | 1.90% | 27.14% | 42.38% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.00% | 0.65% | NA |
| Indica III | 913 | 94.20% | 0.00% | 0.33% | 5.48% | NA |
| Indica Intermediate | 786 | 94.30% | 0.00% | 1.53% | 4.20% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 58.30% | 0.00% | 5.21% | 36.46% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 1.11% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000477694 | G -> A | LOC_Os10g01730.1 | downstream_gene_variant ; 1640.0bp to feature; MODIFIER | silent_mutation | Average:22.141; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477694 | G -> A | LOC_Os10g01750.1 | downstream_gene_variant ; 4990.0bp to feature; MODIFIER | silent_mutation | Average:22.141; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477694 | G -> A | LOC_Os10g01740.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.141; most accessible tissue: Callus, score: 37.292 | N | N | N | N |
| vg1000477694 | G -> DEL | N | N | silent_mutation | Average:22.141; most accessible tissue: Callus, score: 37.292 | N | N | N | N |