| Variant ID: vg0314254707 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14254707 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCTTTTCAGAGTCAACAATTACAAGGTACTTCCTTCTTCTTACTACTTTTATTTTCTGATTCAATGCAAGAAAAACTTCATAAGTCTTCAATTTCTCGA[C/A]
CTCAATCAATTGTAATCTTGTTGTCCTCTTAAGTTCAACTTGGAACTTTTTGAATATTTTTGAATTGTACAGCTTGACAGCTTGGTACTCAATGTAGTAA
TTACTACATTGAGTACCAAGCTGTCAAGCTGTACAATTCAAAAATATTCAAAAAGTTCCAAGTTGAACTTAAGAGGACAACAAGATTACAATTGATTGAG[G/T]
TCGAGAAATTGAAGACTTATGAAGTTTTTCTTGCATTGAATCAGAAAATAAAAGTAGTAAGAAGAAGGAAGTACCTTGTAATTGTTGACTCTGAAAAGGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 0.20% | 1.31% | 0.51% | NA |
| All Indica | 2759 | 96.70% | 0.30% | 2.25% | 0.80% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 93.90% | 0.00% | 5.21% | 0.84% | NA |
| Indica II | 465 | 94.40% | 0.00% | 3.44% | 2.15% | NA |
| Indica III | 913 | 98.70% | 0.50% | 0.33% | 0.44% | NA |
| Indica Intermediate | 786 | 97.70% | 0.40% | 1.53% | 0.38% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314254707 | C -> A | LOC_Os03g24970.1 | missense_variant ; p.Val60Phe; MODERATE | nonsynonymous_codon ; V60F | Average:6.655; most accessible tissue: Callus, score: 16.966 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0314254707 | C -> DEL | LOC_Os03g24970.1 | N | frameshift_variant | Average:6.655; most accessible tissue: Callus, score: 16.966 | N | N | N | N |