| Variant ID: vg0510478449 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478449 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGCAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTATTTTGTAAACACGAT[T/C]
CTAGAACTGTACAATATTATTTATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCT
AGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATAAATAATATTGTACAGTTCTAG[A/G]
ATCGTGTTTACAAAATAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTGCA
| 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 | 87.90% | 1.30% | 10.85% | 0.00% | NA |
| All Indica | 2759 | 86.60% | 1.00% | 12.43% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.40% | 0.00% | NA |
| Aus | 269 | 30.50% | 12.30% | 57.25% | 0.00% | NA |
| Indica I | 595 | 92.60% | 0.20% | 7.23% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.40% | 1.29% | 0.00% | NA |
| Indica III | 913 | 76.50% | 2.40% | 21.14% | 0.00% | NA |
| Indica Intermediate | 786 | 86.80% | 0.40% | 12.85% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 10.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478449 | T -> C | LOC_Os05g18210.1 | downstream_gene_variant ; 1282.0bp to feature; MODIFIER | silent_mutation | Average:19.353; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478449 | T -> C | LOC_Os05g18230.1 | downstream_gene_variant ; 2699.0bp to feature; MODIFIER | silent_mutation | Average:19.353; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |
| vg0510478449 | T -> C | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.353; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 | N | N | N | N |