| Variant ID: vg1012224308 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224308 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGACGCCATGAGGAGGAACGAGATCGACAAGGTCCC[C/T]
GGCTGCAGCCTCATCGAGATCGACGGCGTTGTGCACGAATTCAAAGCAATCCCAGCAAATTCCATCCGATAAAAACTCAAGAAGATTCATCAAAGAACAG
CTGTTCTTTGATGAATCTTCTTGAGTTTTTATCGGATGGAATTTGCTGGGATTGCTTTGAATTCGTGCACAACGCCGTCGATCTCGATGAGGCTGCAGCC[G/A]
GGGACCTTGTCGATCTCGTTCCTCCTCATGGCGTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGG
| 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 | 50.00% | 0.00% | 0.91% | 49.03% | NA |
| All Indica | 2759 | 33.50% | 0.00% | 1.16% | 65.35% | NA |
| All Japonica | 1512 | 89.00% | 0.10% | 0.07% | 10.85% | NA |
| Aus | 269 | 11.50% | 0.00% | 2.60% | 85.87% | NA |
| Indica I | 595 | 15.30% | 0.00% | 0.34% | 84.37% | NA |
| Indica II | 465 | 42.20% | 0.00% | 1.94% | 55.91% | NA |
| Indica III | 913 | 35.90% | 0.10% | 1.64% | 62.32% | NA |
| Indica Intermediate | 786 | 39.20% | 0.00% | 0.76% | 60.05% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 82.10% | 0.20% | 0.20% | 17.46% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 1.04% | 89.58% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224308 | C -> T | LOC_Os10g23830.1 | synonymous_variant ; p.Pro134Pro; LOW | synonymous_codon | Average:14.196; most accessible tissue: Callus, score: 56.934 | N | N | N | N |
| vg1012224308 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.196; most accessible tissue: Callus, score: 56.934 | N | N | N | N |