| Variant ID: vg0128509427 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509427 |
| 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: 53. )
CTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGG[C/T]
AGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGA
TCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCT[G/A]
CCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAG
| 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 | 48.50% | 1.90% | 4.85% | 44.79% | NA |
| All Indica | 2759 | 31.10% | 3.20% | 7.68% | 58.06% | NA |
| All Japonica | 1512 | 90.00% | 0.00% | 0.13% | 9.85% | NA |
| Aus | 269 | 3.00% | 0.00% | 3.35% | 93.68% | NA |
| Indica I | 595 | 5.70% | 3.40% | 5.88% | 85.04% | NA |
| Indica II | 465 | 32.70% | 2.40% | 7.53% | 57.42% | NA |
| Indica III | 913 | 51.60% | 3.90% | 10.73% | 33.73% | NA |
| Indica Intermediate | 786 | 25.40% | 2.70% | 5.60% | 66.28% | NA |
| Temperate Japonica | 767 | 93.20% | 0.00% | 0.13% | 6.65% | NA |
| Tropical Japonica | 504 | 82.10% | 0.00% | 0.20% | 17.66% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 2.08% | 81.25% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 4.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509427 | C -> T | LOC_Os01g49570.1 | synonymous_variant ; p.Leu49Leu; LOW | synonymous_codon | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |
| vg0128509427 | C -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |