| Variant ID: vg0234907959 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34907959 |
| Reference Allele: GA | Alternative Allele: G,GAA |
| Primary Allele: GA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGTGGCCCATGGCTACTGCCACTACTGAATTGTCAGTTGAGTTCTTTGAACATGGAATGTGTAGAGACATTGAATCCTTTCAGAAATCTCACCTAGAAT[GA/G,GAA]
AAAAAAAATAAGCATGCTTGGAAACATACGAGCAATTTGAAGTTTGAGAAAGAGGGTAGTTTTAAGTTATGGCTATCAAATAACTTACAGTTCTTTCATT
AATGAAAGAACTGTAAGTTATTTGATAGCCATAACTTAAAACTACCCTCTTTCTCAAACTTCAAATTGCTCGTATGTTTCCAAGCATGCTTATTTTTTTT[TC/C,TTC]
ATTCTAGGTGAGATTTCTGAAAGGATTCAATGTCTCTACACATTCCATGTTCAAAGAACTCAACTGACAATTCAGTAGTGGCAGTAGCCATGGGCCACAG
| Populations | Population Size | Frequency of GA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.40% | 1.10% | 0.80% | 1.59% | GAA: 0.08% |
| All Indica | 2759 | 99.70% | 0.00% | 0.11% | 0.18% | NA |
| All Japonica | 1512 | 94.50% | 3.40% | 1.72% | 0.07% | GAA: 0.26% |
| Aus | 269 | 74.00% | 0.00% | 2.97% | 23.05% | 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 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.38% | 0.51% | NA |
| Temperate Japonica | 767 | 93.00% | 4.60% | 2.48% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 2.60% | 1.19% | 0.20% | GAA: 0.60% |
| Japonica Intermediate | 241 | 97.50% | 1.70% | 0.41% | 0.00% | GAA: 0.41% |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234907959 | GA -> G | LOC_Os02g56960.1 | upstream_gene_variant ; 3070.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> G | LOC_Os02g56940.1 | downstream_gene_variant ; 4057.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> G | LOC_Os02g56940.2 | downstream_gene_variant ; 4057.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> G | LOC_Os02g56940.3 | downstream_gene_variant ; 4057.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> G | LOC_Os02g56950.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> G | LOC_Os02g56950.2 | intron_variant ; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56960.1 | upstream_gene_variant ; 3069.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56940.1 | downstream_gene_variant ; 4058.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56940.2 | downstream_gene_variant ; 4058.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56940.3 | downstream_gene_variant ; 4058.0bp to feature; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56950.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> GAA | LOC_Os02g56950.2 | intron_variant ; MODIFIER | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
| vg0234907959 | GA -> DEL | N | N | silent_mutation | Average:46.467; most accessible tissue: Callus, score: 86.944 | N | N | N | N |
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