| Variant ID: vg0314254696 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14254696 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGTGTATTCCTCCTTTTCAGAGTCAACAATTACAAGGTACTTCCTTCTTCTTACTACTTTTATTTTCTGATTCAATGCAAGAAAAACTTCATAAGTCTT[C/T]
AATTTCTCGACCTCAATCAATTGTAATCTTGTTGTCCTCTTAAGTTCAACTTGGAACTTTTTGAATATTTTTGAATTGTACAGCTTGACAGCTTGGTACT
AGTACCAAGCTGTCAAGCTGTACAATTCAAAAATATTCAAAAAGTTCCAAGTTGAACTTAAGAGGACAACAAGATTACAATTGATTGAGGTCGAGAAATT[G/A]
AAGACTTATGAAGTTTTTCTTGCATTGAATCAGAAAATAAAAGTAGTAAGAAGAAGGAAGTACCTTGTAATTGTTGACTCTGAAAAGGAGGAATACACTT
| 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 | 80.80% | 10.90% | 6.67% | 1.67% | NA |
| All Indica | 2759 | 67.80% | 18.40% | 10.95% | 2.83% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.40% | 0.00% | 2.23% | 0.37% | NA |
| Indica I | 595 | 68.60% | 16.00% | 11.76% | 3.70% | NA |
| Indica II | 465 | 70.30% | 12.70% | 13.76% | 3.23% | NA |
| Indica III | 913 | 67.10% | 25.30% | 5.48% | 2.08% | NA |
| Indica Intermediate | 786 | 66.40% | 15.80% | 15.01% | 2.80% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 5.60% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314254696 | C -> T | LOC_Os03g24970.1 | synonymous_variant ; p.Leu63Leu; LOW | synonymous_codon | Average:6.655; most accessible tissue: Callus, score: 16.966 | N | N | N | N |
| vg0314254696 | C -> DEL | LOC_Os03g24970.1 | N | frameshift_variant | Average:6.655; most accessible tissue: Callus, score: 16.966 | N | N | N | N |