| Variant ID: vg0621394333 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 21394333 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 404. )
TAAACTTCTCATAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTCATGCAACATTGTAGATAGACATTGAGTGTCCAAATCTATGGTCTCTCCACCTAA[A/C]
GGAGAAGGTACGAACATGCCTTCTCGAGCTGCGGCGGTGTTCTCTACATCCTGATCCAACACTTCTTCAGCTGCGACATCAGGCGCCTCTTGCTCTCCAT
ATGGAGAGCAAGAGGCGCCTGATGTCGCAGCTGAAGAAGTGTTGGATCAGGATGTAGAGAACACCGCCGCAGCTCGAGAAGGCATGTTCGTACCTTCTCC[T/G]
TTAGGTGGAGAGACCATAGATTTGGACACTCAATGTCTATCTACAATGTTGCATGACATTGAAGACGCAGAGGACAACGACAGAGATTATGAGAAGTTTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.30% | 0.00% | 2.67% | 97.06% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 0.29% | 99.28% | NA |
| All Japonica | 1512 | 0.10% | 0.00% | 7.41% | 92.53% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.17% | 99.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 1.51% | 97.42% | NA |
| Indica III | 913 | 0.50% | 0.00% | 0.00% | 99.45% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 0.00% | 99.87% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 2.48% | 97.52% | NA |
| Tropical Japonica | 504 | 0.20% | 0.00% | 12.90% | 86.90% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 11.62% | 88.38% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 6.67% | 93.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0621394333 | A -> C | LOC_Os06g36440.1 | synonymous_variant ; p.Pro110Pro; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0621394333 | A -> DEL | LOC_Os06g36440.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |