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Detailed information for vg0410565265:
| Variant ID: vg0410565265 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565265 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCATACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGT[C/G]
GACAAGGTCGAGGTCGGCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTCCATCGAGACTATTGGCGGCTATTAAATGCCGATTCTATACTACCAA
Reverse complement sequence
TTGGTAGTATAGAATCGGCATTTAATAGCCGCCAATAGTCTCGATGGAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGCCGACCTCGACCTTGTC[G/C]
ACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGGGAGTATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.10% | 0.10% | 0.59% | 59.18% | NA |
| All Indica | 2759 | 8.80% | 0.10% | 0.76% | 90.36% | NA |
| All Japonica | 1512 | 99.20% | 0.00% | 0.13% | 0.66% | NA |
| Aus | 269 | 5.20% | 0.00% | 0.74% | 94.05% | NA |
| Indica I | 595 | 5.00% | 0.00% | 0.67% | 94.29% | NA |
| Indica II | 465 | 25.80% | 0.00% | 0.65% | 73.55% | NA |
| Indica III | 913 | 2.40% | 0.00% | 0.77% | 96.82% | NA |
| Indica Intermediate | 786 | 9.00% | 0.30% | 0.89% | 89.82% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.26% | 0.13% | 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 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 57.80% | 3.30% | 3.33% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565265 | C -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565265 | C -> G | LOC_Os04g19010.1 | missense_variant ; p.Asp20His; MODERATE | nonsynonymous_codon ; D20H | Average:9.854; most accessible tissue: Callus, score: 40.877 | probably damaging  |
2.425 |
DELETERIOUS | 0.05 |