| Variant ID: vg1218480868 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480868 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTTGTGAACTTCCAAGTAATCTGATCCGGTTCTCCAACATCTAAGTGCACATTTCGGACCGCTTCCCACAGTGCGACTAGCTGTTCGACGAGGTCGACT[G/A]
CGATAGATGATTGTGAATCAAGCTTAAAATCTTGCACCTAGGCGTCCTCCTCCTTTCCTTGCCGAAGGGATTTTCCTCTGTTTTTTGAGATCGCAAAGAC
GTCTTTGCGATCTCAAAAAACAGAGGAAAATCCCTTCGGCAAGGAAAGGAGGAGGACGCCTAGGTGCAAGATTTTAAGCTTGATTCACAATCATCTATCG[C/T]
AGTCGACCTCGTCGAACAGCTAGTCGCACTGTGGGAAGCGGTCCGAAATGTGCACTTAGATGTTGGAGAACCGGATCAGATTACTTGGAAGTTCACAAAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.30% | 0.20% | 4.17% | 82.35% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 2.46% | 94.93% | NA |
| All Japonica | 1512 | 34.50% | 0.50% | 0.26% | 64.68% | NA |
| Aus | 269 | 2.60% | 0.00% | 43.12% | 54.28% | NA |
| Indica I | 595 | 3.00% | 0.00% | 2.02% | 94.96% | NA |
| Indica II | 465 | 4.10% | 0.00% | 1.94% | 93.98% | NA |
| Indica III | 913 | 1.10% | 0.00% | 2.08% | 96.82% | NA |
| Indica Intermediate | 786 | 3.20% | 0.00% | 3.56% | 93.26% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.39% | 39.77% | NA |
| Tropical Japonica | 504 | 2.80% | 0.20% | 0.20% | 96.83% | NA |
| Japonica Intermediate | 241 | 20.30% | 2.90% | 0.00% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 6.25% | 93.75% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 3.33% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480868 | G -> DEL | N | N | silent_mutation | Average:6.762; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480868 | G -> A | LOC_Os12g30780.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:6.762; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480868 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1555.0bp to feature; MODIFIER | silent_mutation | Average:6.762; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480868 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 4038.0bp to feature; MODIFIER | silent_mutation | Average:6.762; most accessible tissue: Callus, score: 17.698 | N | N | N | N |