| Variant ID: vg0410565194 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565194 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAAGAGAACCAGGCTCATCTACCACAACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTC[C/T]
GGAGAGTATTCTCGTGTGTGAGCATACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGA
TCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGGGAGTATGCTCACACACGAGAATACTCTCC[G/A]
GAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTTGTGGTAGATGAGCCTGGTTCTCTTT
| 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 | 39.90% | 0.00% | 0.87% | 59.23% | NA |
| All Indica | 2759 | 8.60% | 0.00% | 1.09% | 90.29% | NA |
| All Japonica | 1512 | 99.20% | 0.10% | 0.07% | 0.66% | NA |
| Aus | 269 | 3.30% | 0.00% | 2.23% | 94.42% | NA |
| Indica I | 595 | 4.90% | 0.00% | 1.01% | 94.12% | NA |
| Indica II | 465 | 24.90% | 0.00% | 1.51% | 73.55% | NA |
| Indica III | 913 | 2.50% | 0.00% | 0.66% | 96.82% | NA |
| Indica Intermediate | 786 | 8.80% | 0.10% | 1.40% | 89.69% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 2.08% | 11.46% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565194 | C -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.934; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565194 | C -> T | LOC_Os04g19010.1 | synonymous_variant ; p.Pro43Pro; LOW | synonymous_codon | Average:9.934; most accessible tissue: Callus, score: 40.877 | N | N | N | N |