| Variant ID: vg1218481138 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481138 |
| Reference Allele: G | Alternative Allele: T,C |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCCCCTATTGTTATGTTTGTTGAGGCGGCGAAGATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCC[G/T,C]
GCCTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCC
GGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAGGC[C/A,G]
GGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGATCTTCGCCGCCTCAACAAACATAACAATAGGGGAC
| 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 | 34.80% | 0.30% | 7.09% | 57.81% | C: 0.04% |
| All Indica | 2759 | 31.30% | 0.00% | 6.67% | 61.98% | C: 0.07% |
| All Japonica | 1512 | 40.80% | 0.00% | 3.11% | 56.08% | NA |
| Aus | 269 | 33.10% | 0.00% | 28.62% | 38.29% | NA |
| Indica I | 595 | 24.00% | 0.00% | 2.52% | 73.45% | NA |
| Indica II | 465 | 34.00% | 0.00% | 6.02% | 59.78% | C: 0.22% |
| Indica III | 913 | 35.50% | 0.00% | 7.78% | 56.74% | NA |
| Indica Intermediate | 786 | 30.30% | 0.00% | 8.91% | 60.69% | C: 0.13% |
| Temperate Japonica | 767 | 62.10% | 0.00% | 1.04% | 36.90% | NA |
| Tropical Japonica | 504 | 12.70% | 0.00% | 6.15% | 81.15% | NA |
| Japonica Intermediate | 241 | 32.00% | 0.00% | 3.32% | 64.73% | NA |
| VI/Aromatic | 96 | 27.10% | 14.60% | 19.79% | 38.54% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481138 | G -> C | LOC_Os12g30770.1 | upstream_gene_variant ; 1825.0bp to feature; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> C | LOC_Os12g30790.1 | downstream_gene_variant ; 3768.0bp to feature; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> C | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> DEL | N | N | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1825.0bp to feature; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3768.0bp to feature; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1218481138 | G -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.338; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |