| Variant ID: vg1223515223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23515223 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTACAAGAGACCCAGACGATCAAGATGTCGTGCGGTGGAAGTTGCAACTGCGGTTCCTGCGGATGCGGCGGTGGCTGCGGGTACGTTCGATCTTCAGCTA[T/C]
TGATTCTGAATATGTTTGCTATGTATTTGTCAACATAAACTGTCATAAGCTTTGATGATTTTGATGTACTTTCCATCATAGAAGAATACTATGTTAGCCC
GGGCTAACATAGTATTCTTCTATGATGGAAAGTACATCAAAATCATCAAAGCTTATGACAGTTTATGTTGACAAATACATAGCAAACATATTCAGAATCA[A/G]
TAGCTGAAGATCGAACGTACCCGCAGCCACCGCCGCATCCGCAGGAACCGCAGTTGCAACTTCCACCGCACGACATCTTGATCGTCTGGGTCTCTTGTAA
| 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 | 98.70% | 1.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223515223 | T -> C | LOC_Os12g38310.1 | upstream_gene_variant ; 1429.0bp to feature; MODIFIER | silent_mutation | Average:58.523; most accessible tissue: Minghui63 root, score: 91.928 | N | N | N | N |
| vg1223515223 | T -> C | LOC_Os12g38280.1 | downstream_gene_variant ; 4642.0bp to feature; MODIFIER | silent_mutation | Average:58.523; most accessible tissue: Minghui63 root, score: 91.928 | N | N | N | N |
| vg1223515223 | T -> C | LOC_Os12g38290.1 | downstream_gene_variant ; 1746.0bp to feature; MODIFIER | silent_mutation | Average:58.523; most accessible tissue: Minghui63 root, score: 91.928 | N | N | N | N |
| vg1223515223 | T -> C | LOC_Os12g38320.1 | downstream_gene_variant ; 4745.0bp to feature; MODIFIER | silent_mutation | Average:58.523; most accessible tissue: Minghui63 root, score: 91.928 | N | N | N | N |
| vg1223515223 | T -> C | LOC_Os12g38300.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.523; most accessible tissue: Minghui63 root, score: 91.928 | N | N | N | N |