| Variant ID: vg1222419894 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22419894 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTACACACACAAATTTCCAACTTTTCCGTCACATCATTCCAATTTTAACCAAATTTCTAATTTTGGCGTTGATTTGATATGATTTGACAATGTGATGCTA[C/T]
CGTAAATATTTGCTAATGACAGATTAATTAGGCTTAATAGATTCGTCTCGCAGTTTATATGCGGAATTTATAATTTGTTTTGTTATTAGTCTACATTTAA
TTAAATGTAGACTAATAACAAAACAAATTATAAATTCCGCATATAAACTGCGAGACGAATCTATTAAGCCTAATTAATCTGTCATTAGCAAATATTTACG[G/A]
TAGCATCACATTGTCAAATCATATCAAATCAACGCCAAAATTAGAAATTTGGTTAAAATTGGAATGATGTGACGGAAAAGTTGGAAATTTGTGTGTGTAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 0.40% | 0.93% | 42.55% | NA |
| All Indica | 2759 | 38.80% | 0.80% | 1.20% | 59.22% | NA |
| All Japonica | 1512 | 87.00% | 0.00% | 0.13% | 12.90% | NA |
| Aus | 269 | 37.50% | 0.00% | 2.97% | 59.48% | NA |
| Indica I | 595 | 39.70% | 1.80% | 1.51% | 56.97% | NA |
| Indica II | 465 | 22.20% | 0.00% | 1.08% | 76.77% | NA |
| Indica III | 913 | 45.30% | 0.30% | 1.10% | 53.23% | NA |
| Indica Intermediate | 786 | 40.50% | 0.90% | 1.15% | 57.51% | NA |
| Temperate Japonica | 767 | 91.40% | 0.00% | 0.13% | 8.47% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 0.20% | 20.83% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 0.00% | 10.37% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222419894 | C -> DEL | N | N | silent_mutation | Average:6.436; most accessible tissue: Callus, score: 19.452 | N | N | N | N |
| vg1222419894 | C -> T | LOC_Os12g36600.1 | downstream_gene_variant ; 4278.0bp to feature; MODIFIER | silent_mutation | Average:6.436; most accessible tissue: Callus, score: 19.452 | N | N | N | N |
| vg1222419894 | C -> T | LOC_Os12g36610.1 | downstream_gene_variant ; 629.0bp to feature; MODIFIER | silent_mutation | Average:6.436; most accessible tissue: Callus, score: 19.452 | N | N | N | N |
| vg1222419894 | C -> T | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.436; most accessible tissue: Callus, score: 19.452 | N | N | N | N |