| Variant ID: vg1222420538 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22420538 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 77. )
TGTGCTTCTACGTCAGTATCTGGTGACGAAATCTTGGTGTTACTCGCTTCTGTTGCTGCTGCTTATATTTCTTTCCTTGTAGGAAGTGTTTCTTCGAGCA[C/T]
CTGAAAAGTTGATGGTATTATATATATCAGCTAAGGGAATCAAAAGCAAAGGATATATTACCCCGTATTACATATTTGCATATCTGAAGTTAGTAAAGAA
TTCTTTACTAACTTCAGATATGCAAATATGTAATACGGGGTAATATATCCTTTGCTTTTGATTCCCTTAGCTGATATATATAATACCATCAACTTTTCAG[G/A]
TGCTCGAAGAAACACTTCCTACAAGGAAAGAAATATAAGCAGCAGCAACAGAAGCGAGTAACACCAAGATTTCGTCACCAGATACTGACGTAGAAGCACA
| 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 | 38.80% | 17.50% | 0.47% | 43.31% | NA |
| All Indica | 2759 | 10.40% | 28.60% | 0.58% | 60.38% | NA |
| All Japonica | 1512 | 86.40% | 0.70% | 0.20% | 12.76% | NA |
| Aus | 269 | 32.70% | 4.50% | 0.74% | 62.08% | NA |
| Indica I | 595 | 10.80% | 29.60% | 0.50% | 59.16% | NA |
| Indica II | 465 | 4.70% | 17.20% | 0.43% | 77.63% | NA |
| Indica III | 913 | 10.80% | 34.30% | 0.55% | 54.33% | NA |
| Indica Intermediate | 786 | 13.10% | 28.00% | 0.76% | 58.14% | NA |
| Temperate Japonica | 767 | 91.40% | 0.10% | 0.13% | 8.34% | NA |
| Tropical Japonica | 504 | 77.40% | 1.20% | 0.40% | 21.03% | NA |
| Japonica Intermediate | 241 | 89.20% | 1.20% | 0.00% | 9.54% | NA |
| VI/Aromatic | 96 | 92.70% | 2.10% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 67.80% | 13.30% | 1.11% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222420538 | C -> DEL | N | N | silent_mutation | Average:13.735; most accessible tissue: Callus, score: 90.472 | N | N | N | N |
| vg1222420538 | C -> T | LOC_Os12g36600.1 | downstream_gene_variant ; 4922.0bp to feature; MODIFIER | silent_mutation | Average:13.735; most accessible tissue: Callus, score: 90.472 | N | N | N | N |
| vg1222420538 | C -> T | LOC_Os12g36610.1 | downstream_gene_variant ; 1273.0bp to feature; MODIFIER | silent_mutation | Average:13.735; most accessible tissue: Callus, score: 90.472 | N | N | N | N |
| vg1222420538 | C -> T | LOC_Os12g36620.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.735; most accessible tissue: Callus, score: 90.472 | N | N | N | N |