| Variant ID: vg0227216783 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 27216783 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACAGTGGAAAAGCCAAAAAGAAGAAGAGAAAAACAACAGTCGCATCAGCACCCGACGTGCCGACCACTAAACATGCACACTGCCTACTGACGAACCATT[G/T]
CATGAACATTTTAATACCAACAAGATCAACACCATTTCTTCATCAATCACAAGGTGGCATCCCATTTTGTCAGCGAAGAAAGATTTGACTCATGCATCTC
GAGATGCATGAGTCAAATCTTTCTTCGCTGACAAAATGGGATGCCACCTTGTGATTGATGAAGAAATGGTGTTGATCTTGTTGGTATTAAAATGTTCATG[C/A]
AATGGTTCGTCAGTAGGCAGTGTGCATGTTTAGTGGTCGGCACGTCGGGTGCTGATGCGACTGTTGTTTTTCTCTTCTTCTTTTTGGCTTTTCCACTGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.17% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.53% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.40% | 0.70% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0227216783 | G -> T | LOC_Os02g44910.1 | upstream_gene_variant ; 4136.0bp to feature; MODIFIER | N | Average:70.873; most accessible tissue: Callus, score: 89.914 | N | N | N | N |
| vg0227216783 | G -> T | LOC_Os02g44920.1 | intron_variant ; MODIFIER | N | Average:70.873; most accessible tissue: Callus, score: 89.914 | N | N | N | N |