| Variant ID: vg1218481011 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481011 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTCCTCCTCCTTTCCTTGCCGAAGGGATTTTCCTCTGTTTTTTGAGATCGCAAAGACAAGCGGCATGAGGTCTTTGGGTCTTTGCCCACCAATCCATGC[G/A]
GACTCCCAAAATCGCACCGTGTTTCCGTCCCCTATTGTTATGTTTGTTGAGGCGGCGAAGATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTT
AACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGATCTTCGCCGCCTCAACAAACATAACAATAGGGGACGGAAACACGGTGCGATTTTGGGAGTC[C/T]
GCATGGATTGGTGGGCAAAGACCCAAAGACCTCATGCCGCTTGTCTTTGCGATCTCAAAAAACAGAGGAAAATCCCTTCGGCAAGGAAAGGAGGAGGACG
| 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 | 12.70% | 0.10% | 0.89% | 86.25% | NA |
| All Indica | 2759 | 1.80% | 0.00% | 0.40% | 97.75% | NA |
| All Japonica | 1512 | 34.50% | 0.40% | 0.66% | 64.42% | NA |
| Aus | 269 | 1.10% | 0.00% | 7.43% | 91.45% | NA |
| Indica I | 595 | 2.50% | 0.00% | 0.00% | 97.48% | NA |
| Indica II | 465 | 2.80% | 0.00% | 0.43% | 96.77% | NA |
| Indica III | 913 | 0.40% | 0.00% | 0.22% | 99.34% | NA |
| Indica Intermediate | 786 | 2.40% | 0.00% | 0.89% | 96.69% | NA |
| Temperate Japonica | 767 | 59.10% | 0.00% | 1.04% | 39.90% | NA |
| Tropical Japonica | 504 | 2.60% | 1.20% | 0.20% | 96.03% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 0.41% | 76.35% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 1.11% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481011 | G -> DEL | N | N | silent_mutation | Average:26.936; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg1218481011 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1698.0bp to feature; MODIFIER | silent_mutation | Average:26.936; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg1218481011 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3895.0bp to feature; MODIFIER | silent_mutation | Average:26.936; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg1218481011 | G -> A | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.936; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |