| Variant ID: vg0510478395 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478395 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACTGAGTACAACCACCGTACTCAACAAGACACACCCACAAATGCAGAATAAATGCAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGC[A/T]
GTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTAAACACGATTCTAGAACTGTACAATATTATTTATCAAGGCCGTGAACCCACACGAA
TTCGTGTGGGTTCACGGCCTTGATAAATAATATTGTACAGTTCTAGAATCGTGTTTACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTAC[T/A]
GCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTGCATTTATTCTGCATTTGTGGGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.30% | 9.80% | 3.32% | 0.57% | NA |
| All Indica | 2759 | 84.70% | 9.70% | 4.64% | 0.98% | NA |
| All Japonica | 1512 | 99.50% | 0.20% | 0.26% | 0.00% | NA |
| Aus | 269 | 23.40% | 68.40% | 8.18% | 0.00% | NA |
| Indica I | 595 | 92.30% | 0.80% | 6.72% | 0.17% | NA |
| Indica II | 465 | 97.60% | 0.90% | 1.08% | 0.43% | NA |
| Indica III | 913 | 73.30% | 21.10% | 4.16% | 1.42% | NA |
| Indica Intermediate | 786 | 84.60% | 8.30% | 5.73% | 1.40% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478395 | A -> T | LOC_Os05g18210.1 | downstream_gene_variant ; 1228.0bp to feature; MODIFIER | silent_mutation | Average:20.53; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0510478395 | A -> T | LOC_Os05g18230.1 | downstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:20.53; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0510478395 | A -> T | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.53; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0510478395 | A -> DEL | N | N | silent_mutation | Average:20.53; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |