| Variant ID: vg0327370609 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370609 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTGCAGGGTGACGCACGGCATGGTGGACTCCGCCATGGACCCGAGGAGCTCCATCTTGAACACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATG[A/G]
AACGTCTCGCTGCCGACGGAGAACAACACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAG
CTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCGCGGACCGTGCCGACGGCTCGGACGTGTTGTTCTCCGTCGGCAGCGAGACGTT[T/C]
CATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAAGATGGAGCTCCTCGGGTCCATGGCGGAGTCCACCATGCCGTGCGTCACCCTGCACA
| 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 | 65.50% | 34.20% | 0.04% | 0.23% | NA |
| All Indica | 2759 | 98.00% | 1.70% | 0.04% | 0.25% | NA |
| All Japonica | 1512 | 1.30% | 98.50% | 0.00% | 0.20% | NA |
| Aus | 269 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.30% | 1.10% | 0.00% | 0.65% | NA |
| Indica III | 913 | 97.60% | 2.20% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 97.50% | 2.30% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 0.50% | 99.20% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 1.80% | 98.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 34.40% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370609 | A -> DEL | LOC_Os03g48120.1 | N | frameshift_variant | Average:79.641; most accessible tissue: Zhenshan97 panicle, score: 90.268 | N | N | N | N |
| vg0327370609 | A -> G | LOC_Os03g48120.1 | synonymous_variant ; p.Phe61Phe; LOW | synonymous_codon | Average:79.641; most accessible tissue: Zhenshan97 panicle, score: 90.268 | N | N | N | N |