| Variant ID: vg1200353021 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 353021 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )
GCTGGCTGTTAAGTTCAAAATAACTTAAATTTCTGAGCATGTGTTCTGAAATTCAGCCTGATGCATATGATCTGCTGTGGTTATTCAAGTATAGTTACTT[A/AT]
TTTTATTGTTACTATGGTTTGTTTCTTGTTTAAGACAATAAATTTATTCGACTCAAATTATAAGAAACTAATACTCTGGTGCTTACAGTTGCTGGTAACC
GGTTACCAGCAACTGTAAGCACCAGAGTATTAGTTTCTTATAATTTGAGTCGAATAAATTTATTGTCTTAAACAAGAAACAAACCATAGTAACAATAAAA[T/AT]
AAGTAACTATACTTGAATAACCACAGCAGATCATATGCATCAGGCTGAATTTCAGAACACATGCTCAGAAATTTAAGTTATTTTGAACTTAACAGCCAGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.70% | 14.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 89.80% | 10.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200353021 | A -> AT | LOC_Os12g01574.1 | upstream_gene_variant ; 2377.0bp to feature; MODIFIER | silent_mutation | Average:48.144; most accessible tissue: Callus, score: 79.374 | N | N | N | N |
| vg1200353021 | A -> AT | LOC_Os12g01570.1 | downstream_gene_variant ; 3877.0bp to feature; MODIFIER | silent_mutation | Average:48.144; most accessible tissue: Callus, score: 79.374 | N | N | N | N |
| vg1200353021 | A -> AT | LOC_Os12g01590.1 | downstream_gene_variant ; 2501.0bp to feature; MODIFIER | silent_mutation | Average:48.144; most accessible tissue: Callus, score: 79.374 | N | N | N | N |
| vg1200353021 | A -> AT | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.144; most accessible tissue: Callus, score: 79.374 | N | N | N | N |
| vg1200353021 | A -> AT | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:48.144; most accessible tissue: Callus, score: 79.374 | N | N | N | N |