| Variant ID: vg0814383017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14383017 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGCTGGAGGAGTTCCCTCCCGGGACCGAGGACGACGCGCGCGCGCGGGTCGGGGATGCTGCCGACCACATCGTCAACGGCTTCGAGGGCTCGGCCCCTCG[G/A]
CTCGCGTTCGCCCCCGACTCCGACGAGGAGGGGAACGCCAGCAGTGGAAGCGACGGTGGCAACGAGGCCGGCGACCTGGGCGCGTCAGAATGAGCCCCCA
TGGGGGCTCATTCTGACGCGCCCAGGTCGCCGGCCTCGTTGCCACCGTCGCTTCCACTGCTGGCGTTCCCCTCCTCGTCGGAGTCGGGGGCGAACGCGAG[C/T]
CGAGGGGCCGAGCCCTCGAAGCCGTTGACGATGTGGTCGGCAGCATCCCCGACCCGCGCGCGCGCGTCGTCCTCGGTCCCGGGAGGGAACTCCTCCAGCG
| 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 | 37.30% | 0.10% | 18.35% | 44.18% | NA |
| All Indica | 2759 | 25.60% | 0.10% | 22.83% | 51.43% | NA |
| All Japonica | 1512 | 66.10% | 0.10% | 7.74% | 25.99% | NA |
| Aus | 269 | 6.30% | 0.40% | 34.20% | 59.11% | NA |
| Indica I | 595 | 19.30% | 0.30% | 20.17% | 60.17% | NA |
| Indica II | 465 | 23.70% | 0.00% | 19.57% | 56.77% | NA |
| Indica III | 913 | 31.30% | 0.20% | 26.07% | 42.39% | NA |
| Indica Intermediate | 786 | 24.80% | 0.00% | 23.03% | 52.16% | NA |
| Temperate Japonica | 767 | 93.50% | 0.00% | 1.43% | 5.08% | NA |
| Tropical Japonica | 504 | 36.30% | 0.40% | 16.87% | 46.43% | NA |
| Japonica Intermediate | 241 | 41.50% | 0.00% | 8.71% | 49.79% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 15.62% | 77.08% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 14.44% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814383017 | G -> A | LOC_Os08g23760.1 | synonymous_variant ; p.Arg1014Arg; LOW | synonymous_codon | Average:5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |
| vg0814383017 | G -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:5.318; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |