| Variant ID: vg0221510347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21510347 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGAGTGATCGGCGTCCCCCGGCCGGGCTCCGTTCCGCTGGCCACGGGCGATGGCACAGAGCTGCCTAACCCGTGGAACATCGAACACCTTCGTCGCTTC[T/A]
ACCCCTAAAGGGGATCGGGTGTCAGGTTTCGGGCTCGGGCCAACCCCGCACCCCCCTCGGGCGTGCAGGGTTGGCCGGGGGCTACCACATATGCATATTC
GAATATGCATATGTGGTAGCCCCCGGCCAACCCTGCACGCCCGAGGGGGGTGCGGGGTTGGCCCGAGCCCGAAACCTGACACCCGATCCCCTTTAGGGGT[A/T]
GAAGCGACGAAGGTGTTCGATGTTCCACGGGTTAGGCAGCTCTGTGCCATCGCCCGTGGCCAGCGGAACGGAGCCCGGCCGGGGGACGCCGATCACTCGA
| 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 | 35.20% | 0.10% | 0.15% | 64.56% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 0.11% | 97.64% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.07% | 3.24% | NA |
| Aus | 269 | 1.90% | 0.00% | 0.00% | 98.14% | NA |
| Indica I | 595 | 2.20% | 0.00% | 0.00% | 97.82% | NA |
| Indica II | 465 | 2.20% | 0.00% | 0.00% | 97.85% | NA |
| Indica III | 913 | 1.60% | 0.00% | 0.22% | 98.14% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 0.13% | 96.82% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 93.30% | 0.00% | 0.00% | 6.75% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 89.60% | 2.10% | 2.08% | 6.25% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 1.11% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510347 | T -> A | LOC_Os02g35780.1 | downstream_gene_variant ; 4858.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510347 | T -> A | LOC_Os02g35790.1 | downstream_gene_variant ; 2838.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510347 | T -> A | LOC_Os02g35810.1 | downstream_gene_variant ; 2685.0bp to feature; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510347 | T -> A | LOC_Os02g35800.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0221510347 | T -> DEL | N | N | silent_mutation | Average:7.969; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |