| Variant ID: vg0123776332 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776332 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACAGCCAGGAGTAGAAGGGAACTTCGTTGACAGGCAAGCAGTTGCATACCCTGGAGTTTACTCTTCCATTATCAAAATAAAACAGTGACAGCCTTAAAAA[T/A]
TTTCTTTGACGTGCAACAGAGGGAGATTCAGAGTAGCTAAAGTTGATATTGACACATATTGCAGTCTGTAATACTGACATGTTCGAGGAATCTCTTCCAA
TTGGAAGAGATTCCTCGAACATGTCAGTATTACAGACTGCAATATGTGTCAATATCAACTTTAGCTACTCTGAATCTCCCTCTGTTGCACGTCAAAGAAA[A/T]
TTTTTAAGGCTGTCACTGTTTTATTTTGATAATGGAAGAGTAAACTCCAGGGTATGCAACTGCTTGCCTGTCAACGAAGTTCCCTTCTACTCCTGGCTGT
| 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 | 43.20% | 1.70% | 1.86% | 53.22% | NA |
| All Indica | 2759 | 11.50% | 0.00% | 2.90% | 85.54% | NA |
| All Japonica | 1512 | 87.40% | 5.30% | 0.40% | 6.88% | NA |
| Aus | 269 | 92.60% | 0.00% | 0.37% | 7.06% | NA |
| Indica I | 595 | 4.40% | 0.00% | 2.18% | 93.45% | NA |
| Indica II | 465 | 7.10% | 0.00% | 4.30% | 88.60% | NA |
| Indica III | 913 | 13.00% | 0.00% | 2.19% | 84.78% | NA |
| Indica Intermediate | 786 | 17.80% | 0.10% | 3.44% | 78.63% | NA |
| Temperate Japonica | 767 | 99.30% | 0.30% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 74.40% | 6.30% | 0.99% | 18.25% | NA |
| Japonica Intermediate | 241 | 76.80% | 19.10% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776332 | T -> A | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 170.0bp to feature; MODIFIER | silent_mutation | Average:41.392; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0123776332 | T -> A | LOC_Os01g41920.1 | upstream_gene_variant ; 3649.0bp to feature; MODIFIER | silent_mutation | Average:41.392; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0123776332 | T -> A | LOC_Os01g41910.1 | downstream_gene_variant ; 4817.0bp to feature; MODIFIER | silent_mutation | Average:41.392; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0123776332 | T -> DEL | N | N | silent_mutation | Average:41.392; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |