| Variant ID: vg1218481201 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481201 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGGCCTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTC[C/T]
GCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTC
GACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGC[G/A]
GACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAGGCCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAA
| 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 | 17.90% | 0.60% | 6.94% | 74.61% | NA |
| All Indica | 2759 | 7.50% | 0.70% | 8.70% | 83.07% | NA |
| All Japonica | 1512 | 36.60% | 0.50% | 0.99% | 61.97% | NA |
| Aus | 269 | 9.70% | 0.00% | 19.33% | 71.00% | NA |
| Indica I | 595 | 8.60% | 0.20% | 4.87% | 86.39% | NA |
| Indica II | 465 | 8.60% | 1.10% | 7.10% | 83.23% | NA |
| Indica III | 913 | 4.60% | 0.70% | 11.72% | 83.02% | NA |
| Indica Intermediate | 786 | 9.40% | 1.00% | 9.03% | 80.53% | NA |
| Temperate Japonica | 767 | 60.20% | 0.10% | 0.91% | 38.72% | NA |
| Tropical Japonica | 504 | 5.40% | 1.00% | 1.19% | 92.46% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.40% | 0.83% | 72.20% | NA |
| VI/Aromatic | 96 | 28.10% | 0.00% | 14.58% | 57.29% | NA |
| Intermediate | 90 | 34.40% | 1.10% | 7.78% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481201 | C -> DEL | N | N | silent_mutation | Average:36.541; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg1218481201 | C -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1888.0bp to feature; MODIFIER | silent_mutation | Average:36.541; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg1218481201 | C -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3705.0bp to feature; MODIFIER | silent_mutation | Average:36.541; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg1218481201 | C -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.541; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |