| Variant ID: vg0512023190 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023190 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 204. )
CAGCAGCGACATGATTTACACGAGCCTTGGATGCTGGTACAGCAGAGTTATTCTGGGCAGGGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGC[A/G]
TAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCCCTCTTGGCAGGTTGTTGCTGTGCTGGAGCTGCAACAGGACGTGGAG
CTCCACGTCCTGTTGCAGCTCCAGCACAGCAACAACCTGCCAAGAGGGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTA[T/C]
GCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCCCTGCCCAGAATAACTCTGCTGTACCAGCATCCAAGGCTCGTGTAAATCATGTCGCTGCTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.30% | 0.40% | 6.75% | 5.54% | NA |
| All Indica | 2759 | 86.60% | 0.40% | 8.41% | 4.64% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.07% | 0.20% | NA |
| Aus | 269 | 21.90% | 2.60% | 28.62% | 46.84% | NA |
| Indica I | 595 | 92.30% | 0.00% | 7.23% | 0.50% | NA |
| Indica II | 465 | 98.30% | 0.20% | 1.08% | 0.43% | NA |
| Indica III | 913 | 77.10% | 0.80% | 15.12% | 7.01% | NA |
| Indica Intermediate | 786 | 86.40% | 0.30% | 5.85% | 7.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 6.67% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023190 | A -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:30.544; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg0512023190 | A -> G | LOC_Os05g20480.1 | synonymous_variant ; p.Tyr91Tyr; LOW | synonymous_codon | Average:30.544; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |