| Variant ID: vg0910529820 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10529820 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTCCTCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCAT[C/T]
CCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTCACA
TGTGAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGG[G/A]
ATGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGAGGAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 0.60% | 2.41% | 21.82% | NA |
| All Indica | 2759 | 88.40% | 0.10% | 2.17% | 9.31% | NA |
| All Japonica | 1512 | 47.50% | 1.40% | 3.24% | 47.88% | NA |
| Aus | 269 | 97.40% | 0.00% | 0.37% | 2.23% | NA |
| Indica I | 595 | 91.10% | 0.00% | 2.86% | 6.05% | NA |
| Indica II | 465 | 80.60% | 0.40% | 1.29% | 17.63% | NA |
| Indica III | 913 | 91.10% | 0.00% | 1.10% | 7.78% | NA |
| Indica Intermediate | 786 | 87.80% | 0.10% | 3.44% | 8.65% | NA |
| Temperate Japonica | 767 | 52.40% | 0.30% | 2.35% | 44.98% | NA |
| Tropical Japonica | 504 | 48.80% | 3.80% | 2.98% | 44.44% | NA |
| Japonica Intermediate | 241 | 29.00% | 0.00% | 6.64% | 64.32% | NA |
| VI/Aromatic | 96 | 76.00% | 1.00% | 4.17% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529820 | C -> DEL | N | N | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529820 | C -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |