| Variant ID: vg1001933229 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933229 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCATGTCAGATATCATATTGGCTGTTATCAATGATCCACCCAATACTACTGCAAGATCATTTGCAACTGAGACCATCTTTGGATGGTCCTTTTGGTCGGT[C/T]
GCTAGCATCTTGAAAAGGTAGCTGTACTCCTCCTGTGATAAACTATTTAGATGAACTGCCTTTGCTGTTCCGAACCTTGCAAGATTTTCAATCCTACTTA
TAAGTAGGATTGAAAATCTTGCAAGGTTCGGAACAGCAAAGGCAGTTCATCTAAATAGTTTATCACAGGAGGAGTACAGCTACCTTTTCAAGATGCTAGC[G/A]
ACCGACCAAAAGGACCATCCAAAGATGGTCTCAGTTGCAAATGATCTTGCAGTAGTATTGGGTGGATCATTGATAACAGCCAATATGATATCTGACATGC
| 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 | 84.90% | 0.10% | 0.42% | 14.56% | NA |
| All Indica | 2759 | 78.40% | 0.00% | 0.43% | 21.20% | NA |
| All Japonica | 1512 | 99.10% | 0.40% | 0.07% | 0.46% | NA |
| Aus | 269 | 65.40% | 0.00% | 2.60% | 31.97% | NA |
| Indica I | 595 | 61.20% | 0.00% | 0.17% | 38.66% | NA |
| Indica II | 465 | 85.40% | 0.00% | 0.65% | 13.98% | NA |
| Indica III | 913 | 81.10% | 0.00% | 0.11% | 18.84% | NA |
| Indica Intermediate | 786 | 84.10% | 0.00% | 0.89% | 15.01% | NA |
| Temperate Japonica | 767 | 98.40% | 0.80% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933229 | C -> T | LOC_Os10g04160.1 | synonymous_variant ; p.Ala218Ala; LOW | synonymous_codon | Average:40.828; most accessible tissue: Callus, score: 77.054 | N | N | N | N |
| vg1001933229 | C -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:40.828; most accessible tissue: Callus, score: 77.054 | N | N | N | N |