| Variant ID: vg0410565233 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565233 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCATACTCCCGGTCACT[C/T]
AGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTCCATCGAGACTATTG
CAATAGTCTCGATGGAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCT[G/A]
AGTGACCGGGAGTATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTT
| 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 | 37.70% | 0.10% | 2.01% | 60.16% | NA |
| All Indica | 2759 | 9.10% | 0.10% | 0.80% | 90.00% | NA |
| All Japonica | 1512 | 91.70% | 0.00% | 4.03% | 4.30% | NA |
| Aus | 269 | 5.60% | 0.00% | 0.37% | 94.05% | NA |
| Indica I | 595 | 5.70% | 0.00% | 0.50% | 93.78% | NA |
| Indica II | 465 | 26.00% | 0.00% | 1.08% | 72.90% | NA |
| Indica III | 913 | 3.00% | 0.00% | 0.66% | 96.39% | NA |
| Indica Intermediate | 786 | 8.80% | 0.40% | 1.02% | 89.82% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.91% | 0.65% | NA |
| Tropical Japonica | 504 | 82.10% | 0.00% | 8.13% | 9.72% | NA |
| Japonica Intermediate | 241 | 90.00% | 0.00% | 5.39% | 4.56% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 3.12% | 11.46% | NA |
| Intermediate | 90 | 53.30% | 3.30% | 8.89% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565233 | C -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565233 | C -> T | LOC_Os04g19010.1 | synonymous_variant ; p.Leu30Leu; LOW | synonymous_codon | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |