| Variant ID: vg1213095502 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095502 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
AAGAAGACAACGATTTCAACCATCAGAATAAAAAAGGGCAGCCTCAAACTCCACTCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTA[C/A]
ACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACATACAGAAGAAGCTGTAGATACGGAATCACCAACTACCATTCTATACATATG
CATATGTATAGAATGGTAGTTGGTGATTCCGTATCTACAGCTTCTTCTGTATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGT[G/T]
TACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGAGTGGAGTTTGAGGCTGCCCTTTTTTATTCTGATGGTTGAAATCGTTGTCTTCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.60% | 0.00% | 0.40% | 10.94% | NA |
| All Indica | 2759 | 82.00% | 0.00% | 0.62% | 17.36% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.13% | 2.31% | 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 | 60.40% | 0.00% | 1.72% | 37.85% | NA |
| Indica III | 913 | 81.80% | 0.10% | 0.33% | 17.74% | NA |
| Indica Intermediate | 786 | 82.20% | 0.00% | 0.64% | 17.18% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.26% | 4.04% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095502 | C -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:66.162; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |
| vg1213095502 | C -> A | LOC_Os12g23150.1 | missense_variant ; p.Cys208Phe; MODERATE | nonsynonymous_codon ; C208F | Average:66.162; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | unknown | unknown | DELETERIOUS | 0.00 |