| Variant ID: vg1218481172 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481172 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGGCCTCCCATGGCTATATAAAGGACCCCCTAGTC[G/T]
TCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCC
GGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGA[C/A]
GACTAGGGGGTCCTTTATATAGCCATGGGAGGCCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.70% | 0.10% | 5.73% | 57.38% | NA |
| All Indica | 2759 | 31.30% | 0.30% | 6.63% | 61.80% | NA |
| All Japonica | 1512 | 42.40% | 0.00% | 2.12% | 55.49% | NA |
| Aus | 269 | 47.20% | 0.00% | 14.87% | 37.92% | NA |
| Indica I | 595 | 23.50% | 0.30% | 2.69% | 73.45% | NA |
| Indica II | 465 | 34.00% | 0.00% | 6.02% | 60.00% | NA |
| Indica III | 913 | 35.70% | 0.10% | 8.11% | 56.08% | NA |
| Indica Intermediate | 786 | 30.50% | 0.50% | 8.27% | 60.69% | NA |
| Temperate Japonica | 767 | 62.70% | 0.00% | 0.65% | 36.64% | NA |
| Tropical Japonica | 504 | 14.70% | 0.00% | 4.76% | 80.56% | NA |
| Japonica Intermediate | 241 | 35.70% | 0.00% | 1.24% | 63.07% | NA |
| VI/Aromatic | 96 | 58.30% | 0.00% | 8.33% | 33.33% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 8.89% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481172 | G -> DEL | N | N | silent_mutation | Average:35.18; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481172 | G -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1859.0bp to feature; MODIFIER | silent_mutation | Average:35.18; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481172 | G -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3734.0bp to feature; MODIFIER | silent_mutation | Average:35.18; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481172 | G -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.18; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |