| Variant ID: vg0139512926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512926 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )
GTATCTCAAACCTGTGCTGTTGGGTACCTTGCACTAGAGCTCGATGTTTCATAGCCTTTTTACGCAACTCCTCTAGCTTTTTCTGCATGAAAGCTCCAAA[C/T]
AAAATGCTGTTGTTCGGCATAGAGGGAAGAACTGCCTGGAACCGATCCCTAAAATACCTGCATGTCCCATGTAAAATGAACTCCACTATGCCAACTAGTG
CACTAGTTGGCATAGTGGAGTTCATTTTACATGGGACATGCAGGTATTTTAGGGATCGGTTCCAGGCAGTTCTTCCCTCTATGCCGAACAACAGCATTTT[G/A]
TTTGGAGCTTTCATGCAGAAAAAGCTAGAGGAGTTGCGTAAAAAGGCTATGAAACATCGAGCTCTAGTGCAAGGTACCCAACAGCACAGGTTTGAGATAC
| 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 | 25.30% | 0.10% | 1.71% | 72.87% | NA |
| All Indica | 2759 | 1.30% | 0.20% | 1.52% | 97.03% | NA |
| All Japonica | 1512 | 74.20% | 0.00% | 0.40% | 25.40% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.23% | 97.03% | NA |
| Indica I | 595 | 2.90% | 0.00% | 0.50% | 96.64% | NA |
| Indica II | 465 | 1.10% | 1.10% | 0.43% | 97.42% | NA |
| Indica III | 913 | 0.20% | 0.00% | 0.99% | 98.80% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 3.56% | 95.04% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 51.80% | 0.00% | 0.40% | 47.82% | NA |
| Japonica Intermediate | 241 | 48.10% | 0.00% | 1.66% | 50.21% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 23.96% | 75.00% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 4.44% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512926 | C -> T | LOC_Os01g67990.1 | synonymous_variant ; p.Leu656Leu; LOW | synonymous_codon | Average:11.257; most accessible tissue: Callus, score: 20.75 | N | N | N | N |
| vg0139512926 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:11.257; most accessible tissue: Callus, score: 20.75 | N | N | N | N |