| Variant ID: vg0510478441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478441 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGAATAAATGCAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTA[A/C]
ACACGATTCTAGAACTGTACAATATTATTTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAAC
GTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAAATAATATTGTACAGTTCTAGAATCGTGT[T/G]
TACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTGCATTTATTCT
| 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 | 99.50% | 0.20% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.20% | 0.00% | NA |
| Aus | 269 | 94.10% | 3.30% | 2.60% | 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 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.39% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478441 | A -> C | LOC_Os05g18210.1 | downstream_gene_variant ; 1274.0bp to feature; MODIFIER | silent_mutation | Average:18.928; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| vg0510478441 | A -> C | LOC_Os05g18230.1 | downstream_gene_variant ; 2707.0bp to feature; MODIFIER | silent_mutation | Average:18.928; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| vg0510478441 | A -> C | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.928; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |