| Variant ID: vg0910657418 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657418 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGACGGGCCGTCGCCCAGGGCAACCTCCTTGACTGGGACCTCGTCGCACGTGACCATCCGCTGCCTTGGGGCGGCCGGGACGGAGGTGCTGAGCCTCTC[G/A]
TCGCCACCCGCGGGCTTGGACGCCGCGGCGAGATGGTCCGCGCGCTGCTCCATACAAGCAAGCGCGACTTTGAGGTCGCCATGGTCGGTGATGGGGCCAC
GTGGCCCCATCACCGACCATGGCGACCTCAAAGTCGCGCTTGCTTGTATGGAGCAGCGCGCGGACCATCTCGCCGCGGCGTCCAAGCCCGCGGGTGGCGA[C/T]
GAGAGGCTCAGCACCTCCGTCCCGGCCGCCCCAAGGCAGCGGATGGTCACGTGCGACGAGGTCCCAGTCAAGGAGGTTGCCCTGGGCGACGGCCCGTCCA
| 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 | 55.30% | 0.50% | 10.75% | 33.50% | NA |
| All Indica | 2759 | 50.50% | 0.10% | 14.93% | 34.40% | NA |
| All Japonica | 1512 | 63.60% | 1.30% | 5.03% | 30.16% | NA |
| Aus | 269 | 60.60% | 0.00% | 3.35% | 36.06% | NA |
| Indica I | 595 | 57.30% | 0.00% | 6.05% | 36.64% | NA |
| Indica II | 465 | 38.50% | 0.00% | 13.55% | 47.96% | NA |
| Indica III | 913 | 52.40% | 0.10% | 23.66% | 23.88% | NA |
| Indica Intermediate | 786 | 50.40% | 0.40% | 12.34% | 36.90% | NA |
| Temperate Japonica | 767 | 77.80% | 0.00% | 1.96% | 20.21% | NA |
| Tropical Japonica | 504 | 47.80% | 3.60% | 6.35% | 42.26% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.40% | 12.03% | 36.51% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 3.12% | 48.96% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 8.89% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657418 | G -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:7.299; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg0910657418 | G -> A | LOC_Os09g17420.1 | synonymous_variant ; p.Asp151Asp; LOW | synonymous_codon | Average:7.299; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |