| Variant ID: vg0510478451 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478451 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTAAACACGATTC[T/C]
AGAACTGTACAATATTATTTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGG
CCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAAATAATATTGTACAGTTCT[A/G]
GAATCGTGTTTACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.20% | 0.00% | 7.74% | 0.04% | NA |
| All Indica | 2759 | 92.60% | 0.00% | 7.25% | 0.07% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 42.00% | 0.00% | 57.99% | 0.00% | NA |
| Indica I | 595 | 93.30% | 0.20% | 6.39% | 0.17% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 87.40% | 0.00% | 12.60% | 0.00% | NA |
| Indica Intermediate | 786 | 94.40% | 0.00% | 5.47% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478451 | T -> DEL | N | N | silent_mutation | Average:19.3; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478451 | T -> C | LOC_Os05g18210.1 | downstream_gene_variant ; 1284.0bp to feature; MODIFIER | silent_mutation | Average:19.3; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478451 | T -> C | LOC_Os05g18230.1 | downstream_gene_variant ; 2697.0bp to feature; MODIFIER | silent_mutation | Average:19.3; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478451 | T -> C | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.3; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |