| Variant ID: vg0219100431 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19100431 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTTTAGCAGGAACACAAGTTTGAGCAAGTCAAATGAATTACAATGGATTCTAACAATATCACCCATTTCCTGGGTCCAAATTAACTCAAGTGGCCCAAA[C/T]
ATTTATGAAAATAAGCAATTACTCAATTGGTATGACCCACCACTTGTAGAAATTTTTACTTGACTATACAGAACAGCTAACCAAGGGAACAATTGATTTG
CAAATCAATTGTTCCCTTGGTTAGCTGTTCTGTATAGTCAAGTAAAAATTTCTACAAGTGGTGGGTCATACCAATTGAGTAATTGCTTATTTTCATAAAT[G/A]
TTTGGGCCACTTGAGTTAATTTGGACCCAGGAAATGGGTGATATTGTTAGAATCCATTGTAATTCATTTGACTTGCTCAAACTTGTGTTCCTGCTAAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.40% | 1.20% | 0.34% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.10% | 0.58% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 0.50% | 1.18% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.10% | 0.43% | 0.00% | NA |
| Indica III | 913 | 95.10% | 4.80% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.30% | 0.90% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0219100431 | C -> T | LOC_Os02g32340.1 | upstream_gene_variant ; 3015.0bp to feature; MODIFIER | silent_mutation | Average:53.101; most accessible tissue: Callus, score: 73.155 | N | N | N | N |
| vg0219100431 | C -> T | LOC_Os02g32350.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.101; most accessible tissue: Callus, score: 73.155 | N | N | N | N |
| vg0219100431 | C -> T | LOC_Os02g32350.2 | intron_variant ; MODIFIER | silent_mutation | Average:53.101; most accessible tissue: Callus, score: 73.155 | N | N | N | N |