| Variant ID: vg0228080520 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28080520 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 336. )
ATCCAACTGCAGCTATCATAGGCTTTAAAAACTGCGTTCTCCGAACAAGTGTCAAGAAACCTTCTTCGGTAGCAGAAAATGCCCCTCGAACAACTTCCTC[C/T]
GATACTGTTTCACTTTCTCGGGCAAGTCCTAGAAAGATAGGAAAGGTTGAGCAGTCATTTTGGTGCACTGAACAATTTCGGTTGAGATATGCTTGCCATT
AATGGCAAGCATATCTCAACCGAAATTGTTCAGTGCACCAAAATGACTGCTCAACCTTTCCTATCTTTCTAGGACTTGCCCGAGAAAGTGAAACAGTATC[G/A]
GAGGAAGTTGTTCGAGGGGCATTTTCTGCTACCGAAGAAGGTTTCTTGACACTTGTTCGGAGAACGCAGTTTTTAAAGCCTATGATAGCTGCAGTTGGAT
| 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 | 92.60% | 7.10% | 0.06% | 0.23% | NA |
| All Indica | 2759 | 93.00% | 6.60% | 0.07% | 0.33% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 45.70% | 53.20% | 0.37% | 0.74% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.10% | 6.50% | 0.00% | 0.43% | NA |
| Indica III | 913 | 91.90% | 7.70% | 0.22% | 0.22% | NA |
| Indica Intermediate | 786 | 89.10% | 10.30% | 0.00% | 0.64% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0228080520 | C -> T | LOC_Os02g46080.1 | synonymous_variant ; p.Ser113Ser; LOW | synonymous_codon | Average:62.471; most accessible tissue: Callus, score: 89.557 | N | N | N | N |
| vg0228080520 | C -> T | LOC_Os02g46080.2 | synonymous_variant ; p.Ser113Ser; LOW | synonymous_codon | Average:62.471; most accessible tissue: Callus, score: 89.557 | N | N | N | N |
| vg0228080520 | C -> DEL | LOC_Os02g46080.1 | N | frameshift_variant | Average:62.471; most accessible tissue: Callus, score: 89.557 | N | N | N | N |
| vg0228080520 | C -> DEL | LOC_Os02g46080.2 | N | frameshift_variant | Average:62.471; most accessible tissue: Callus, score: 89.557 | N | N | N | N |