| Variant ID: vg0607894551 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7894551 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTCTATCGCCCCACTGAACACAGAGCCCCTTCTGCAGGCCTTGGCCACCGCAAACACCACGATGTTGGATGGGTTAAGTGCCCAGGTGGAGGCCCTGCA[G/A]
GCAGAGCGGGCGGAGCTCGACGCCGCGTGGGCGCGTGTCGAAGAGGGGCGACGCTCGGTGGAGGCCATGGTGGAGGTGGGCCGTAAGGCTCACCGCCGGC
GCCGGCGGTGAGCCTTACGGCCCACCTCCACCATGGCCTCCACCGAGCGTCGCCCCTCTTCGACACGCGCCCACGCGGCGTCGAGCTCCGCCCGCTCTGC[C/T]
TGCAGGGCCTCCACCTGGGCACTTAACCCATCCAACATCGTGGTGTTTGCGGTGGCCAAGGCCTGCAGAAGGGGCTCTGTGTTCAGTGGGGCGATAGAAG
| 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 | 8.40% | 0.10% | 4.32% | 87.13% | NA |
| All Indica | 2759 | 1.10% | 0.20% | 1.92% | 96.77% | NA |
| All Japonica | 1512 | 23.10% | 0.10% | 6.42% | 70.44% | NA |
| Aus | 269 | 0.00% | 0.00% | 14.13% | 85.87% | NA |
| Indica I | 595 | 0.20% | 0.30% | 0.84% | 98.66% | NA |
| Indica II | 465 | 1.30% | 0.00% | 1.29% | 97.42% | NA |
| Indica III | 913 | 1.60% | 0.30% | 2.52% | 95.51% | NA |
| Indica Intermediate | 786 | 1.00% | 0.10% | 2.42% | 96.44% | NA |
| Temperate Japonica | 767 | 37.00% | 0.00% | 5.08% | 57.89% | NA |
| Tropical Japonica | 504 | 6.90% | 0.20% | 7.54% | 85.32% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 8.30% | 79.25% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 10.42% | 86.46% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 6.67% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607894551 | G -> A | LOC_Os06g14150.1 | synonymous_variant ; p.Gln673Gln; LOW | synonymous_codon | Average:10.634; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0607894551 | G -> DEL | LOC_Os06g14150.1 | N | frameshift_variant | Average:10.634; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |