| Variant ID: vg0329361287 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361287 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCTCCACGGCACAGGCACGCTCTTCCAGCGCCATGGCACGGGCCTCAAGGGCTTCTTCGCGCCGCCGGGATGCCACCTCGGTCTCCGCCGCCCGCCGTT[C/G]
TCGGGCAGCGGCAGCGTCAAGGACCCCCTGGGCGGCGTCGAGCTTCTTCCCTAGCTCCGCCTCCCAGCTCCCGTATTGAAGGCGGAGGGTGTCCTGCGCC
GGCGCAGGACACCCTCCGCCTTCAATACGGGAGCTGGGAGGCGGAGCTAGGGAAGAAGCTCGACGCCGCCCAGGGGGTCCTTGACGCTGCCGCTGCCCGA[G/C]
AACGGCGGGCGGCGGAGACCGAGGTGGCATCCCGGCGGCGCGAAGAAGCCCTTGAGGCCCGTGCCATGGCGCTGGAAGAGCGTGCCTGTGCCGTGGAGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.70% | 0.10% | 13.37% | 15.81% | NA |
| All Indica | 2759 | 61.70% | 0.30% | 21.46% | 16.60% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 3.00% | 0.00% | 3.35% | 93.68% | NA |
| Indica I | 595 | 59.50% | 1.20% | 24.54% | 14.79% | NA |
| Indica II | 465 | 58.30% | 0.00% | 23.87% | 17.85% | NA |
| Indica III | 913 | 66.70% | 0.00% | 15.01% | 18.29% | NA |
| Indica Intermediate | 786 | 59.50% | 0.00% | 25.19% | 15.27% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 0.00% | 21.88% | 21.88% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 7.78% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361287 | C -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:20.534; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
| vg0329361287 | C -> G | LOC_Os03g51320.1 | missense_variant ; p.Glu693Gln; MODERATE | nonsynonymous_codon ; E693Q | Average:20.534; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | unknown | unknown | DELETERIOUS | 0.00 |