| Variant ID: vg1218481140 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481140 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCCCTATTGTTATGTTTGTTGAGGCGGCGAAGATCCTTTCCTTTTTCCGGCAAATATAAACTTTCCCGAGTTTTTCCCGTCGATGTGGGCTCGATCCCGG[C/G]
CTCCCATGGCTATATAAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTC
GAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTTATATAGCCATGGGAG[G/C]
CCGGGATCGAGCCCACATCGACGGGAAAAACTCGGGAAAGTTTATATTTGCCGGAAAAAGGAAAGGATCTTCGCCGCCTCAACAAACATAACAATAGGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.90% | 0.30% | 7.11% | 57.68% | NA |
| All Indica | 2759 | 31.50% | 0.00% | 6.74% | 61.80% | NA |
| All Japonica | 1512 | 40.90% | 0.00% | 3.04% | 56.08% | NA |
| Aus | 269 | 33.10% | 0.00% | 28.62% | 38.29% | NA |
| Indica I | 595 | 23.90% | 0.00% | 2.69% | 73.45% | NA |
| Indica II | 465 | 34.40% | 0.00% | 5.81% | 59.78% | NA |
| Indica III | 913 | 35.50% | 0.00% | 8.21% | 56.30% | NA |
| Indica Intermediate | 786 | 30.80% | 0.00% | 8.65% | 60.56% | NA |
| Temperate Japonica | 767 | 62.10% | 0.00% | 1.04% | 36.90% | NA |
| Tropical Japonica | 504 | 12.90% | 0.00% | 5.95% | 81.15% | NA |
| Japonica Intermediate | 241 | 32.00% | 0.00% | 3.32% | 64.73% | NA |
| VI/Aromatic | 96 | 27.10% | 15.60% | 19.79% | 37.50% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481140 | C -> DEL | N | N | silent_mutation | Average:34.815; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481140 | C -> G | LOC_Os12g30770.1 | upstream_gene_variant ; 1827.0bp to feature; MODIFIER | silent_mutation | Average:34.815; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481140 | C -> G | LOC_Os12g30790.1 | downstream_gene_variant ; 3766.0bp to feature; MODIFIER | silent_mutation | Average:34.815; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1218481140 | C -> G | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.815; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |