| Variant ID: vg0521668295 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21668295 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTTTCAGCAGGCTTTTATTAGTTTCCGTTATCATTAAAAAATTGTGTCTTTGAGCTGCCAACTGTCTGAGATCTTTCTCAAAATTTACCATTTGACTGCT[A/C]
AAATATTTTTTGGCAACACGAAAAAAATAATGAAAATTAGCAACAAAAATTAGAGATCGACCGCCGTTTTCTTGAATTTACGACCGACCGTAAAATCGAA
TTCGATTTTACGGTCGGTCGTAAATTCAAGAAAACGGCGGTCGATCTCTAATTTTTGTTGCTAATTTTCATTATTTTTTTCGTGTTGCCAAAAAATATTT[T/G]
AGCAGTCAAATGGTAAATTTTGAGAAAGATCTCAGACAGTTGGCAGCTCAAAGACACAATTTTTTAATGATAACGGAAACTAATAAAAGCCTGCTGAAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 80.30% | 19.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0521668295 | A -> C | LOC_Os05g37080.1 | 3_prime_UTR_variant ; 109.0bp to feature; MODIFIER | silent_mutation | Average:61.858; most accessible tissue: Callus, score: 85.035 | N | N | N | N |
| vg0521668295 | A -> C | LOC_Os05g37070.1 | upstream_gene_variant ; 2724.0bp to feature; MODIFIER | silent_mutation | Average:61.858; most accessible tissue: Callus, score: 85.035 | N | N | N | N |