| Variant ID: vg0825346438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25346438 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 313. )
GACGAATGTTGTAGAAATTTGACAACCATGAATGACTTAAACACAGTTCTACCAAGTGTTCAATTGTTAACTCTGTATGTTGCGTGGAAAGAAAGAGGTA[A/G]
ATATACCAACTGACATAATTCAATTTTGGGCTTATCCATTTCCTGAATCTAGGCACTATATAATTATTTGGTGAATTGGTAGAATATATTTTGTGGATTA
TAATCCACAAAATATATTCTACCAATTCACCAAATAATTATATAGTGCCTAGATTCAGGAAATGGATAAGCCCAAAATTGAATTATGTCAGTTGGTATAT[T/C]
TACCTCTTTCTTTCCACGCAACATACAGAGTTAACAATTGAACACTTGGTAGAACTGTGTTTAAGTCATTCATGGTTGTCAAATTTCTACAACATTCGTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.60% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.80% | 1.60% | 0.66% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.50% | 4.60% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825346438 | A -> G | LOC_Os08g40020.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:43.047; most accessible tissue: Callus, score: 83.528 | N | N | N | N |
| vg0825346438 | A -> G | LOC_Os08g40010.1 | downstream_gene_variant ; 2489.0bp to feature; MODIFIER | silent_mutation | Average:43.047; most accessible tissue: Callus, score: 83.528 | N | N | N | N |