| Variant ID: vg1213095553 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095553 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 327. )
CACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACAT[A/T]
CAGAAGAAGCTGTAGATACGGAATCACCAACTACCATTCTATACATATGAAATAGGTGGCGAGTGCTAGTAGGGATCGTAGTTACATCTTTGTCATGCTC
GAGCATGACAAAGATGTAACTACGATCCCTACTAGCACTCGCCACCTATTTCATATGTATAGAATGGTAGTTGGTGATTCCGTATCTACAGCTTCTTCTG[T/A]
ATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.50% | 0.00% | 0.47% | 10.98% | NA |
| All Indica | 2759 | 81.90% | 0.00% | 0.69% | 17.36% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.20% | 2.45% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.00% | 0.17% | 1.01% | NA |
| Indica II | 465 | 60.60% | 0.00% | 1.72% | 37.63% | NA |
| Indica III | 913 | 81.80% | 0.10% | 0.22% | 17.85% | NA |
| Indica Intermediate | 786 | 81.80% | 0.00% | 1.02% | 17.18% | NA |
| Temperate Japonica | 767 | 95.30% | 0.00% | 0.39% | 4.30% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095553 | A -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:69.437; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | N | N | N | N |
| vg1213095553 | A -> T | LOC_Os12g23150.1 | missense_variant ; p.Val191Glu; MODERATE | nonsynonymous_codon ; V191E | Average:69.437; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | unknown | unknown | DELETERIOUS | 0.01 |