| Variant ID: vg0804463333 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4463333 |
| Reference Allele: G | Alternative Allele: GT |
| Primary Allele: G | Secondary Allele: GT |
Inferred Ancestral Allele: Not determined.
TGAATGATATGATGCCCTCAGCGGCTCAGCGGCAAACCGTATGTGCAACTGATATCCAGAACCACGGCTTGTACATGATCGTGTTGTATGCCCATCCAGG[G/GT]
TCCTATATACACGTGCTTGTGTAGGGAAGGTTTAAACGCTAATACCAATTGTAACATCCCTAGCTTCCAAAATCCACATTAACCTAGCTCTTCCATGGAG
CTCCATGGAAGAGCTAGGTTAATGTGGATTTTGGAAGCTAGGGATGTTACAATTGGTATTAGCGTTTAAACCTTCCCTACACAAGCACGTGTATATAGGA[C/AC]
CCTGGATGGGCATACAACACGATCATGTACAAGCCGTGGTTCTGGATATCAGTTGCACATACGGTTTGCCGCTGAGCCGCTGAGGGCATCATATCATTCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.30% | 0.10% | 0.70% | 64.85% | NA |
| All Indica | 2759 | 4.60% | 0.10% | 1.01% | 94.31% | NA |
| All Japonica | 1512 | 95.00% | 0.10% | 0.07% | 4.89% | NA |
| Aus | 269 | 3.00% | 0.00% | 0.37% | 96.65% | NA |
| Indica I | 595 | 6.90% | 0.00% | 1.51% | 91.60% | NA |
| Indica II | 465 | 6.70% | 0.00% | 1.51% | 91.83% | NA |
| Indica III | 913 | 1.50% | 0.00% | 0.11% | 98.36% | NA |
| Indica Intermediate | 786 | 5.20% | 0.30% | 1.40% | 93.13% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 88.70% | 0.00% | 0.00% | 11.31% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 13.50% | 3.10% | 1.04% | 82.29% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 2.22% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463333 | G -> GT | LOC_Os08g07900.1 | upstream_gene_variant ; 3111.0bp to feature; MODIFIER | silent_mutation | Average:9.75; most accessible tissue: Callus, score: 44.628 | N | N | N | N |
| vg0804463333 | G -> GT | LOC_Os08g07910.1 | upstream_gene_variant ; 2213.0bp to feature; MODIFIER | silent_mutation | Average:9.75; most accessible tissue: Callus, score: 44.628 | N | N | N | N |
| vg0804463333 | G -> GT | LOC_Os08g07930.1 | upstream_gene_variant ; 2695.0bp to feature; MODIFIER | silent_mutation | Average:9.75; most accessible tissue: Callus, score: 44.628 | N | N | N | N |
| vg0804463333 | G -> GT | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.75; most accessible tissue: Callus, score: 44.628 | N | N | N | N |
| vg0804463333 | G -> DEL | N | N | silent_mutation | Average:9.75; most accessible tissue: Callus, score: 44.628 | N | N | N | N |