| Variant ID: vg0103668429 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 3668429 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 300. )
ACAAAAAAAAGGCAAAAAAGATCCTGAGAATGACATACAGACTTGTCAAAAAAAAGCTCTATGACGGACGAAACAAAAGGACATATCACAACAAACTGAG[T/A]
GGACATATAAAGCATATTTATGGCCCTTGGGAGGCATTGAAGGAGAGATGTATCTGGTACTGTTAATAATGAGATATTACGAGGAACAAGGTATTTGGTG
CACCAAATACCTTGTTCCTCGTAATATCTCATTATTAACAGTACCAGATACATCTCTCCTTCAATGCCTCCCAAGGGCCATAAATATGCTTTATATGTCC[A/T]
CTCAGTTTGTTGTGATATGTCCTTTTGTTTCGTCCGTCATAGAGCTTTTTTTTGACAAGTCTGTATGTCATTCTCAGGATCTTTTTTGCCTTTTTTTTGT
| 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 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 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 | 64.60% | 35.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0103668429 | T -> A | LOC_Os01g07620.1 | upstream_gene_variant ; 2383.0bp to feature; MODIFIER | silent_mutation | Average:43.654; most accessible tissue: Callus, score: 75.169 | N | N | N | N |
| vg0103668429 | T -> A | LOC_Os01g07610.1 | downstream_gene_variant ; 4110.0bp to feature; MODIFIER | silent_mutation | Average:43.654; most accessible tissue: Callus, score: 75.169 | N | N | N | N |
| vg0103668429 | T -> A | LOC_Os01g07630.1 | intron_variant ; MODIFIER | silent_mutation | Average:43.654; most accessible tissue: Callus, score: 75.169 | N | N | N | N |