| Variant ID: vg1218481154 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481154 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTGTTGAGGCGGCGAAGATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGGCCTCCCATGGCTAT[A/T]
TAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCG
CGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTA[T/A]
ATAGCCATGGGAGGCCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGATCTTCGCCGCCTCAACAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 0.40% | 7.09% | 59.06% | NA |
| All Indica | 2759 | 28.90% | 0.40% | 8.08% | 62.67% | NA |
| All Japonica | 1512 | 38.30% | 0.30% | 2.91% | 58.47% | NA |
| Aus | 269 | 44.60% | 0.00% | 17.10% | 38.29% | NA |
| Indica I | 595 | 23.00% | 0.00% | 3.53% | 73.45% | NA |
| Indica II | 465 | 27.50% | 0.90% | 11.40% | 60.22% | NA |
| Indica III | 913 | 33.50% | 0.30% | 8.65% | 57.50% | NA |
| Indica Intermediate | 786 | 28.60% | 0.50% | 8.91% | 61.96% | NA |
| Temperate Japonica | 767 | 61.70% | 0.10% | 0.91% | 37.29% | NA |
| Tropical Japonica | 504 | 7.30% | 0.80% | 6.35% | 85.52% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 2.07% | 69.29% | NA |
| VI/Aromatic | 96 | 45.80% | 1.00% | 14.58% | 38.54% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 8.89% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481154 | A -> DEL | N | N | silent_mutation | Average:35.06; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481154 | A -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1841.0bp to feature; MODIFIER | silent_mutation | Average:35.06; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481154 | A -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3752.0bp to feature; MODIFIER | silent_mutation | Average:35.06; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481154 | A -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.06; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |