| Variant ID: vg0420967231 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967231 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CCCTTCTCTCGCCGCCGCGACGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGGCCCTCCTCCTCCTCGTCGGGCGTCCCCGC[A/C]
TCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACTTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCT
AGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGA[T/G]
GCGGGGACGCCCGACGAGGAGGAGGAGGGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGTCGCGGCGGCGAGAGAAGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.40% | 0.00% | 27.89% | 59.71% | NA |
| All Indica | 2759 | 4.80% | 0.00% | 22.47% | 72.71% | NA |
| All Japonica | 1512 | 27.80% | 0.00% | 38.43% | 33.73% | NA |
| Aus | 269 | 4.10% | 0.00% | 20.07% | 75.84% | NA |
| Indica I | 595 | 10.90% | 0.00% | 33.78% | 55.29% | NA |
| Indica II | 465 | 1.90% | 0.00% | 7.96% | 90.11% | NA |
| Indica III | 913 | 3.30% | 0.00% | 26.18% | 70.54% | NA |
| Indica Intermediate | 786 | 3.70% | 0.00% | 18.19% | 78.12% | NA |
| Temperate Japonica | 767 | 39.00% | 0.00% | 20.60% | 40.42% | NA |
| Tropical Japonica | 504 | 10.70% | 0.00% | 61.31% | 27.98% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 47.30% | 24.48% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 39.58% | 52.08% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 27.78% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967231 | A -> C | LOC_Os04g34670.1 | 5_prime_UTR_variant ; 7.0bp to feature; MODIFIER | silent_mutation | Average:30.328; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg0420967231 | A -> C | LOC_Os04g34650.1 | upstream_gene_variant ; 2563.0bp to feature; MODIFIER | silent_mutation | Average:30.328; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg0420967231 | A -> DEL | N | N | silent_mutation | Average:30.328; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |