| Variant ID: vg0234178793 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34178793 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 386. )
GGTTCAGAAGCATCCGGCACTATGAGTGGGAGTGCATCGACGAACACCGGCTCAAAGAGATCAAGAACTTCCGGTGTTTGGCAACATTTCGATGAGGTGG[C/T]
CATGACAGGCCCTGATGGAAGGCAGGTAACATTCGCGAGATGTAGAATATGCAAAAATAAGTTATCTGCAAAATCATCTGGTGGAACAGGACATTTGAAG
CTTCAAATGTCCTGTTCCACCAGATGATTTTGCAGATAACTTATTTTTGCATATTCTACATCTCGCGAATGTTACCTGCCTTCCATCAGGGCCTGTCATG[G/A]
CCACCTCATCGAAATGTTGCCAAACACCGGAAGTTCTTGATCTCTTTGAGCCGGTGTTCGTCGATGCACTCCCACTCATAGTGCCGGATGCTTCTGAACC
| 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 | 76.10% | 0.30% | 7.22% | 16.34% | NA |
| All Indica | 2759 | 64.60% | 0.60% | 9.82% | 25.01% | NA |
| All Japonica | 1512 | 95.90% | 0.00% | 2.45% | 1.65% | NA |
| Aus | 269 | 85.10% | 0.00% | 5.95% | 8.92% | NA |
| Indica I | 595 | 42.50% | 1.30% | 16.64% | 39.50% | NA |
| Indica II | 465 | 58.90% | 0.00% | 9.46% | 31.61% | NA |
| Indica III | 913 | 83.00% | 0.00% | 4.93% | 12.05% | NA |
| Indica Intermediate | 786 | 63.20% | 1.00% | 10.56% | 25.19% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 92.70% | 0.00% | 6.75% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 1.24% | 3.73% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 10.42% | 19.79% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 7.78% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178793 | C -> T | LOC_Os02g55830.1 | missense_variant ; p.Ala78Val; MODERATE | nonsynonymous_codon ; A78V | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | TOLERATED | 0.54 |
| vg0234178793 | C -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |