| Variant ID: vg0910529823 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529823 |
| Reference Allele: C | Alternative Allele: A,T |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTCCTCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCATCCC[C/A,T]
CACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTCACACTG
CAGTGTGAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTG[G/T,A]
GGGATGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGAGGAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.90% | 0.20% | 2.05% | 21.79% | T: 0.06% |
| All Indica | 2759 | 88.40% | 0.10% | 2.21% | 9.31% | NA |
| All Japonica | 1512 | 49.70% | 0.10% | 2.18% | 47.82% | T: 0.20% |
| Aus | 269 | 95.90% | 1.50% | 0.37% | 2.23% | NA |
| Indica I | 595 | 91.30% | 0.00% | 2.69% | 6.05% | NA |
| Indica II | 465 | 81.30% | 0.00% | 1.08% | 17.63% | NA |
| Indica III | 913 | 90.80% | 0.20% | 1.20% | 7.78% | NA |
| Indica Intermediate | 786 | 87.70% | 0.00% | 3.69% | 8.65% | NA |
| Temperate Japonica | 767 | 53.10% | 0.00% | 2.09% | 44.85% | NA |
| Tropical Japonica | 504 | 53.20% | 0.40% | 1.59% | 44.44% | T: 0.40% |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 3.73% | 64.32% | T: 0.41% |
| VI/Aromatic | 96 | 79.20% | 0.00% | 2.08% | 18.75% | NA |
| Intermediate | 90 | 70.00% | 1.10% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529823 | C -> DEL | N | N | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529823 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529823 | C -> A | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |