| Variant ID: vg0420967202 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20967202 |
| Reference Allele: C | Alternative Allele: CG |
| Primary Allele: CG | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
GCGCCGGCGGCTCACTAAACCCCAGAACCCCCTTCTCTCGCCGCCGCGACGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGG[C/CG]
CCTCCTCCTCCTCGTCGGGCGTCCCCGCATCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACTTCCGCCTCGTCGCGGACTCCAAGGT
ACCTTGGAGTCCGCGACGAGGCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGATGCGGGGACGCCCGACGAGGAGGAGGAGG[G/CG]
CCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGTCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCGGCGC
| Populations | Population Size | Frequency of CG(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.00% | 0.00% | 18.39% | 54.63% | NA |
| All Indica | 2759 | 23.50% | 0.00% | 9.64% | 66.84% | NA |
| All Japonica | 1512 | 36.20% | 0.00% | 32.94% | 30.89% | NA |
| Aus | 269 | 6.70% | 0.00% | 20.07% | 73.23% | NA |
| Indica I | 595 | 41.20% | 0.00% | 12.27% | 46.55% | NA |
| Indica II | 465 | 8.00% | 0.00% | 6.45% | 85.59% | NA |
| Indica III | 913 | 24.60% | 0.00% | 9.53% | 65.83% | NA |
| Indica Intermediate | 786 | 18.10% | 0.00% | 9.67% | 72.26% | NA |
| Temperate Japonica | 767 | 40.30% | 0.00% | 21.38% | 38.33% | NA |
| Tropical Japonica | 504 | 32.30% | 0.00% | 43.65% | 24.01% | NA |
| Japonica Intermediate | 241 | 31.10% | 0.00% | 47.30% | 21.58% | NA |
| VI/Aromatic | 96 | 44.80% | 0.00% | 22.92% | 32.29% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 32.22% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967202 | C -> CG | LOC_Os04g34670.1 | 5_prime_UTR_variant ; 35.0bp to feature; MODIFIER | silent_mutation | Average:30.069; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0420967202 | C -> CG | LOC_Os04g34650.1 | upstream_gene_variant ; 2535.0bp to feature; MODIFIER | silent_mutation | Average:30.069; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0420967202 | C -> DEL | N | N | silent_mutation | Average:30.069; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |