| Variant ID: vg0304212264 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 4212264 |
| Reference Allele: GAC | Alternative Allele: G |
| Primary Allele: GAC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCATCATCGCAAAATTAACCGGCAAAATCACTGTGGGTGGTCTATTTCCACAGCATCTATCTCAAAATTGATATCTGGAATAACTTAATCTTAAACCTAA[GAC/G]
ACACACAAAAAAAAAACAACTTTTTCTTCATCATCAACACGCACAAAAACATAACACTAGTTATATACAGTGAAGCAAAGCTGCAGAGCAAACAAACCTG
CAGGTTTGTTTGCTCTGCAGCTTTGCTTCACTGTATATAACTAGTGTTATGTTTTTGTGCGTGTTGATGATGAAGAAAAAGTTGTTTTTTTTTTGTGTGT[GTC/C]
TTAGGTTTAAGATTAAGTTATTCCAGATATCAATTTTGAGATAGATGCTGTGGAAATAGACCACCCACAGTGATTTTGCCGGTTAATTTTGCGATGATGC
| Populations | Population Size | Frequency of GAC(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.40% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 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 | 96.90% | 3.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0304212264 | GAC -> G | LOC_Os03g08270.1 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08284.3 | downstream_gene_variant ; 4431.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08270.2 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08270.3 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08270.5 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08270.6 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08284.1 | downstream_gene_variant ; 4431.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08284.2 | downstream_gene_variant ; 4431.0bp to feature; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08280.1 | intron_variant ; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08280.2 | intron_variant ; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |
| vg0304212264 | GAC -> G | LOC_Os03g08280.3 | intron_variant ; MODIFIER | N | Average:73.122; most accessible tissue: Callus, score: 91.123 | N | N | N | N |