| Variant ID: vg1218481143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481143 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTATTGTTATGTTTGTTGAGGCGGCGAAGATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGGCCT[C/T]
CCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCT
AGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGG[G/A]
AGGCCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGATCTTCGCCGCCTCAACAAACATAACAATAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.90% | 1.10% | 13.42% | 63.56% | NA |
| All Indica | 2759 | 14.40% | 1.40% | 17.87% | 66.36% | NA |
| All Japonica | 1512 | 36.70% | 0.60% | 1.72% | 60.98% | NA |
| Aus | 269 | 8.20% | 0.70% | 28.62% | 62.45% | NA |
| Indica I | 595 | 17.60% | 0.20% | 14.62% | 67.56% | NA |
| Indica II | 465 | 9.00% | 3.00% | 17.20% | 70.75% | NA |
| Indica III | 913 | 15.90% | 1.10% | 19.72% | 63.31% | NA |
| Indica Intermediate | 786 | 13.40% | 1.70% | 18.58% | 66.41% | NA |
| Temperate Japonica | 767 | 61.10% | 0.10% | 0.52% | 38.20% | NA |
| Tropical Japonica | 504 | 5.00% | 1.40% | 2.98% | 90.67% | NA |
| Japonica Intermediate | 241 | 25.30% | 0.40% | 2.90% | 71.37% | NA |
| VI/Aromatic | 96 | 27.10% | 1.00% | 27.08% | 44.79% | NA |
| Intermediate | 90 | 40.00% | 2.20% | 13.33% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481143 | C -> DEL | N | N | silent_mutation | Average:34.845; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481143 | C -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1830.0bp to feature; MODIFIER | silent_mutation | Average:34.845; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481143 | C -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3763.0bp to feature; MODIFIER | silent_mutation | Average:34.845; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481143 | C -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.845; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |