| Variant ID: vg0327370717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370717 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGCTGCCGACGGAGAACAACACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTC[G/A]
TCATCACCGGCATATAATATATATTTAAGAAAAGTAAAAATAGGGGGAAACAGTGTGCGCAAGGATATATTCATACACTGACTTGAGAAACATGGCAAGG
CCTTGCCATGTTTCTCAAGTCAGTGTATGAATATATCCTTGCGCACACTGTTTCCCCCTATTTTTACTTTTCTTAAATATATATTATATGCCGGTGATGA[C/T]
GACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCGCGGACCGTGCCGACGGCTCGGACGTGTTGTTCTCCGTCGGCAGCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.50% | 35.30% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 97.90% | 1.90% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 1.30% | 98.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.20% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.20% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 2.00% | 98.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 41.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370717 | G -> A | LOC_Os03g48120.1 | synonymous_variant ; p.Asp25Asp; LOW | synonymous_codon | Average:75.225; most accessible tissue: Zhenshan97 panicle, score: 85.665 | N | N | N | N |