| Variant ID: vg1218480907 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480907 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATCTAAGTGCACATTTCGGACCGCTTCCCACAGTGCGACTAGCTGTTCGACGAGGTCGACTGCGATAGATGATTGTGAATCAAGCTTAAAATCTTGCACC[T/C]
AGGCGTCCTCCTCCTTTCCTTGCCGAAGGGATTTTCCTCTGTTTTTTGAGATCGCAAAGACAAGCGGCATGAGGTCTTTGGGTCTTTGCCCACCAATCCA
TGGATTGGTGGGCAAAGACCCAAAGACCTCATGCCGCTTGTCTTTGCGATCTCAAAAAACAGAGGAAAATCCCTTCGGCAAGGAAAGGAGGAGGACGCCT[A/G]
GGTGCAAGATTTTAAGCTTGATTCACAATCATCTATCGCAGTCGACCTCGTCGAACAGCTAGTCGCACTGTGGGAAGCGGTCCGAAATGTGCACTTAGAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.80% | 0.20% | 0.83% | 86.16% | NA |
| All Indica | 2759 | 1.80% | 0.10% | 0.69% | 97.43% | NA |
| All Japonica | 1512 | 34.90% | 0.10% | 0.60% | 64.35% | NA |
| Aus | 269 | 0.70% | 1.50% | 2.23% | 95.54% | NA |
| Indica I | 595 | 2.70% | 0.00% | 0.50% | 96.81% | NA |
| Indica II | 465 | 3.00% | 0.00% | 0.22% | 96.77% | NA |
| Indica III | 913 | 0.30% | 0.10% | 0.22% | 99.34% | NA |
| Indica Intermediate | 786 | 2.20% | 0.10% | 1.65% | 96.06% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.65% | 39.77% | NA |
| Tropical Japonica | 504 | 3.00% | 0.40% | 0.40% | 96.23% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 0.83% | 75.93% | NA |
| VI/Aromatic | 96 | 0.00% | 3.10% | 2.08% | 94.79% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 3.33% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480907 | T -> C | LOC_Os12g30770.1 | upstream_gene_variant ; 1594.0bp to feature; MODIFIER | silent_mutation | Average:10.786; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1218480907 | T -> C | LOC_Os12g30790.1 | downstream_gene_variant ; 3999.0bp to feature; MODIFIER | silent_mutation | Average:10.786; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1218480907 | T -> C | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.786; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1218480907 | T -> DEL | N | N | silent_mutation | Average:10.786; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |