| Variant ID: vg0510478464 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478464 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTAAACACGATTCTAGAACTGTACAA[T/A]
ATTATTTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTC
GACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAAATAAT[A/T]
TTGTACAGTTCTAGAATCGTGTTTACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.90% | 0.00% | 8.99% | 0.06% | NA |
| All Indica | 2759 | 91.40% | 0.00% | 8.45% | 0.07% | NA |
| All Japonica | 1512 | 98.20% | 0.00% | 1.79% | 0.00% | NA |
| Aus | 269 | 40.90% | 0.00% | 58.74% | 0.37% | NA |
| Indica I | 595 | 93.40% | 0.20% | 6.22% | 0.17% | NA |
| Indica II | 465 | 98.30% | 0.00% | 1.72% | 0.00% | NA |
| Indica III | 913 | 84.60% | 0.00% | 15.44% | 0.00% | NA |
| Indica Intermediate | 786 | 93.90% | 0.00% | 5.98% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 5.36% | 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 | 92.20% | 0.00% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478464 | T -> DEL | N | N | silent_mutation | Average:19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg0510478464 | T -> A | LOC_Os05g18210.1 | downstream_gene_variant ; 1297.0bp to feature; MODIFIER | silent_mutation | Average:19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg0510478464 | T -> A | LOC_Os05g18230.1 | downstream_gene_variant ; 2684.0bp to feature; MODIFIER | silent_mutation | Average:19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |
| vg0510478464 | T -> A | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 | N | N | N | N |