| Variant ID: vg1218481202 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481202 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGGCCTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCC[G/T,A]
CCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCA
TGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGG[C/A,T]
GGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAGGCCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAA
| 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 | 17.70% | 0.60% | 7.05% | 74.46% | A: 0.21% |
| All Indica | 2759 | 7.10% | 0.70% | 8.95% | 82.93% | A: 0.29% |
| All Japonica | 1512 | 36.80% | 0.40% | 0.79% | 61.97% | A: 0.07% |
| Aus | 269 | 10.40% | 0.00% | 19.33% | 70.26% | NA |
| Indica I | 595 | 8.20% | 0.20% | 5.04% | 86.55% | NA |
| Indica II | 465 | 8.80% | 1.10% | 7.31% | 82.80% | NA |
| Indica III | 913 | 4.50% | 0.70% | 11.94% | 82.80% | A: 0.11% |
| Indica Intermediate | 786 | 8.30% | 1.00% | 9.41% | 80.41% | A: 0.89% |
| Temperate Japonica | 767 | 60.60% | 0.00% | 0.52% | 38.85% | NA |
| Tropical Japonica | 504 | 5.20% | 1.00% | 1.19% | 92.46% | A: 0.20% |
| Japonica Intermediate | 241 | 27.00% | 0.40% | 0.83% | 71.78% | NA |
| VI/Aromatic | 96 | 28.10% | 0.00% | 15.62% | 56.25% | NA |
| Intermediate | 90 | 33.30% | 1.10% | 7.78% | 56.67% | A: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481202 | G -> DEL | N | N | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> A | LOC_Os12g30770.1 | upstream_gene_variant ; 1889.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> A | LOC_Os12g30790.1 | downstream_gene_variant ; 3704.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> A | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1889.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3704.0bp to feature; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481202 | G -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.69; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |