| Variant ID: vg0410565281 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565281 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCATACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTC[G/A]
GCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTCCATCGAGACTATTGGCGGCTATTAAATGCCGATTCTATACTACCAACATATGCGTAAAGTTC
GAACTTTACGCATATGTTGGTAGTATAGAATCGGCATTTAATAGCCGCCAATAGTCTCGATGGAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGC[C/T]
GACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGGGAGTATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.80% | 0.10% | 0.99% | 59.10% | NA |
| All Indica | 2759 | 8.60% | 0.10% | 1.41% | 89.89% | NA |
| All Japonica | 1512 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Aus | 269 | 1.90% | 0.40% | 2.23% | 95.54% | NA |
| Indica I | 595 | 4.90% | 0.00% | 1.34% | 93.78% | NA |
| Indica II | 465 | 24.90% | 0.40% | 1.08% | 73.55% | NA |
| Indica III | 913 | 2.60% | 0.00% | 1.31% | 96.06% | NA |
| Indica Intermediate | 786 | 8.50% | 0.30% | 1.78% | 89.44% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 1.11% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565281 | G -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565281 | G -> A | LOC_Os04g19010.1 | synonymous_variant ; p.Ala14Ala; LOW | synonymous_codon | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |