| Variant ID: vg0512023144 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023144 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 200. )
ACAAGAAACGTACCCAAAATCACATCTGGAGCATGTTGAGCTTCTGCAGCAGCGACATGATTTACACGAGCCTTGGATGCTGGTACAGCAGAGTTATTCT[G/A]
GGCAGGGACAACCTTCACGCGTCGGGGCTTCGGACACTTGTCAGCATAATGTCCTGGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCC
GGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCCAGGACATTATGCTGACAAGTGTCCGAAGCCCCGACGCGTGAAGGTTGTCCCTGCC[C/T]
AGAATAACTCTGCTGTACCAGCATCCAAGGCTCGTGTAAATCATGTCGCTGCTGCAGAAGCTCAACATGCTCCAGATGTGATTTTGGGTACGTTTCTTGT
| 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 | 87.70% | 0.20% | 3.98% | 8.19% | NA |
| All Indica | 2759 | 87.40% | 0.00% | 4.68% | 7.90% | NA |
| All Japonica | 1512 | 99.10% | 0.50% | 0.13% | 0.26% | NA |
| Aus | 269 | 22.30% | 0.00% | 18.22% | 59.48% | NA |
| Indica I | 595 | 92.40% | 0.00% | 2.52% | 5.04% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.43% | 1.29% | NA |
| Indica III | 913 | 79.40% | 0.00% | 9.09% | 11.50% | NA |
| Indica Intermediate | 786 | 86.50% | 0.00% | 3.69% | 9.80% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 95.90% | 3.30% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 5.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023144 | G -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:29.174; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 | N | N | N | N |
| vg0512023144 | G -> A | LOC_Os05g20480.1 | stop_gained ; p.Gln107*; HIGH | stop_gained | Average:29.174; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 | N | N | N | N |