| Variant ID: vg0420967182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967182 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAGGCTGTTTGCCGCTACAGCGCCGGCGGCTCACTAAACCCCAGAACCCCCTTCTCTCGCCGCCGCGACGCCGCCCCAATGGCGGTGGACAAATCCGGC[G/A]
GCGGCGGAGGCGGAGGCGGCCCTCCTCCTCCTCGTCGGGCGTCCCCGCATCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACTTCCGC
GCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGATGCGGGGACGCCCGACGAGGAGGAGGAGGGCCGCCTCCGCCTCCGCCGC[C/T]
GCCGGATTTGTCCACCGCCATTGGGGCGGCGTCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCGGCGCTGTAGCGGCAAACAGCCTCG
| 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 | 92.10% | 3.20% | 3.58% | 1.12% | NA |
| All Indica | 2759 | 96.90% | 0.80% | 2.36% | 0.00% | NA |
| All Japonica | 1512 | 93.70% | 0.10% | 2.84% | 3.31% | NA |
| Aus | 269 | 31.60% | 47.60% | 20.82% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 0.40% | 1.72% | 0.00% | NA |
| Indica III | 913 | 95.70% | 0.80% | 3.50% | 0.00% | NA |
| Indica Intermediate | 786 | 95.30% | 1.50% | 3.18% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 84.10% | 0.40% | 7.74% | 7.74% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 1.66% | 4.56% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 93.30% | 1.10% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967182 | G -> DEL | N | N | silent_mutation | Average:27.773; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0420967182 | G -> A | LOC_Os04g34670.1 | 5_prime_UTR_variant ; 56.0bp to feature; MODIFIER | silent_mutation | Average:27.773; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0420967182 | G -> A | LOC_Os04g34650.1 | upstream_gene_variant ; 2514.0bp to feature; MODIFIER | silent_mutation | Average:27.773; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |