| Variant ID: vg0420967226 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967226 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAACCCCCTTCTCTCGCCGCCGCGACGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGGCCCTCCTCCTCCTCGTCGGGCGTC[C/G]
CCGCATCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACTTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGA
TCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGATGCGG[G/C]
GACGCCCGACGAGGAGGAGGAGGGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGTCGCGGCGGCGAGAGAAGGGGGTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.70% | 0.10% | 47.42% | 50.78% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 33.20% | 65.68% | NA |
| All Japonica | 1512 | 3.20% | 0.10% | 67.99% | 28.64% | NA |
| Aus | 269 | 0.40% | 0.00% | 75.09% | 24.54% | NA |
| Indica I | 595 | 1.50% | 0.00% | 50.76% | 47.73% | NA |
| Indica II | 465 | 0.20% | 0.00% | 13.12% | 86.67% | NA |
| Indica III | 913 | 1.40% | 0.00% | 36.47% | 62.10% | NA |
| Indica Intermediate | 786 | 0.90% | 0.10% | 27.99% | 70.99% | NA |
| Temperate Japonica | 767 | 3.80% | 0.10% | 65.06% | 31.03% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 69.44% | 27.18% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.40% | 74.27% | 24.07% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 56.25% | 43.75% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 45.56% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967226 | C -> DEL | N | N | silent_mutation | Average:30.209; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg0420967226 | C -> G | LOC_Os04g34670.1 | 5_prime_UTR_variant ; 12.0bp to feature; MODIFIER | silent_mutation | Average:30.209; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg0420967226 | C -> G | LOC_Os04g34650.1 | upstream_gene_variant ; 2558.0bp to feature; MODIFIER | silent_mutation | Average:30.209; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |