| Variant ID: vg1213095601 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095601 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )
ACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACATACAGAAGAAGCTGTAGATACGGAATCACCAACTACCATTCTATACATA[T/C]
GAAATAGGTGGCGAGTGCTAGTAGGGATCGTAGTTACATCTTTGTCATGCTCCATGTAAAATCCAGGCTTCAGTTCTATCTTCTTGTCTCCATCAGACTG
CAGTCTGATGGAGACAAGAAGATAGAACTGAAGCCTGGATTTTACATGGAGCATGACAAAGATGTAACTACGATCCCTACTAGCACTCGCCACCTATTTC[A/G]
TATGTATAGAATGGTAGTTGGTGATTCCGTATCTACAGCTTCTTCTGTATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.60% | 0.00% | 0.61% | 10.81% | NA |
| All Indica | 2759 | 81.90% | 0.00% | 0.94% | 17.07% | 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 | 60.20% | 0.00% | 2.58% | 37.20% | NA |
| Indica III | 913 | 82.10% | 0.10% | 0.11% | 17.63% | NA |
| Indica Intermediate | 786 | 81.80% | 0.00% | 1.53% | 16.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095601 | T -> C | LOC_Os12g23150.1 | missense_variant ; p.His175Arg; MODERATE | nonsynonymous_codon ; H175R | Average:65.148; most accessible tissue: Minghui63 flower, score: 78.979 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1213095601 | T -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:65.148; most accessible tissue: Minghui63 flower, score: 78.979 | N | N | N | N |