| Variant ID: vg0620602649 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602649 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )
GATTGCTTTAGTGAGTTATAAACACTAAAGTAGATATTAATTGCTTAGACGTAGTGTTTAGGTAATTGTTATACAGTAATTGTTGCAACTTCTTTTTGAG[C/T]
TGTCTGCTCCTCGGGGCGAATTCTATGAGCCACCTCCTTCAAGAGAGAGCAAAGCAATGGTACACCTCTACTGTTGGATGTGTAAGCGGTAGTTGGGAGA
TCTCCCAACTACCGCTTACACATCCAACAGTAGAGGTGTACCATTGCTTTGCTCTCTCTTGAAGGAGGTGGCTCATAGAATTCGCCCCGAGGAGCAGACA[G/A]
CTCAAAAAGAAGTTGCAACAATTACTGTATAACAATTACCTAAACACTACGTCTAAGCAATTAATATCTACTTTAGTGTTTATAACTCACTAAAGCAATC
| 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 | 97.40% | 1.40% | 0.02% | 1.14% | NA |
| All Indica | 2759 | 97.50% | 2.40% | 0.00% | 0.07% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.07% | 3.31% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.10% | 5.80% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.10% | 0.80% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 0.41% | 16.18% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602649 | C -> T | LOC_Os06g35340.1 | synonymous_variant ; p.Ser31Ser; LOW | synonymous_codon | Average:17.216; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0620602649 | C -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:17.216; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |