| Variant ID: vg1218480894 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480894 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCGGTTCTCCAACATCTAAGTGCACATTTCGGACCGCTTCCCACAGTGCGACTAGCTGTTCGACGAGGTCGACTGCGATAGATGATTGTGAATCAAGCTT[A/C]
AAATCTTGCACCTAGGCGTCCTCCTCCTTTCCTTGCCGAAGGGATTTTCCTCTGTTTTTTGAGATCGCAAAGACAAGCGGCATGAGGTCTTTGGGTCTTT
AAAGACCCAAAGACCTCATGCCGCTTGTCTTTGCGATCTCAAAAAACAGAGGAAAATCCCTTCGGCAAGGAAAGGAGGAGGACGCCTAGGTGCAAGATTT[T/G]
AAGCTTGATTCACAATCATCTATCGCAGTCGACCTCGTCGAACAGCTAGTCGCACTGTGGGAAGCGGTCCGAAATGTGCACTTAGATGTTGGAGAACCGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.90% | 0.20% | 3.45% | 83.45% | NA |
| All Indica | 2759 | 2.10% | 0.00% | 1.34% | 96.52% | NA |
| All Japonica | 1512 | 34.50% | 0.50% | 0.20% | 64.75% | NA |
| Aus | 269 | 1.90% | 0.00% | 43.49% | 54.65% | NA |
| Indica I | 595 | 2.70% | 0.00% | 0.34% | 96.97% | NA |
| Indica II | 465 | 4.10% | 0.00% | 1.94% | 93.98% | NA |
| Indica III | 913 | 0.30% | 0.00% | 0.99% | 98.69% | NA |
| Indica Intermediate | 786 | 2.70% | 0.00% | 2.16% | 95.17% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.26% | 39.90% | NA |
| Tropical Japonica | 504 | 2.80% | 0.20% | 0.20% | 96.83% | NA |
| Japonica Intermediate | 241 | 20.30% | 2.90% | 0.00% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 3.33% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480894 | A -> C | LOC_Os12g30770.1 | upstream_gene_variant ; 1581.0bp to feature; MODIFIER | silent_mutation | Average:8.41; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480894 | A -> C | LOC_Os12g30790.1 | downstream_gene_variant ; 4012.0bp to feature; MODIFIER | silent_mutation | Average:8.41; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480894 | A -> C | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.41; most accessible tissue: Callus, score: 17.698 | N | N | N | N |
| vg1218480894 | A -> DEL | N | N | silent_mutation | Average:8.41; most accessible tissue: Callus, score: 17.698 | N | N | N | N |