| Variant ID: vg0430654182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654182 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TATCGGCAAGAAGCTCAACGCCTTGTTCCTGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGCGCCGATAGAGGGTCCCTTCTATCAGCACGTAGCG[T/C]
TTGGAAATGCGTTGGACGCGTTCTGTCACGCTCAGAAATTCCCGAATAGAATTCCAAGCAGAATGTGCATTAAAATCCCCGTCCAGGACCAGCCGGGGTA
TACCCCGGCTGGTCCTGGACGGGGATTTTAATGCACATTCTGCTTGGAATTCTATTCGGGAATTTCTGAGCGTGACAGAACGCGTCCAACGCATTTCCAA[A/G]
CGCTACGTGCTGATAGAAGGGACCCTCTATCGGCGCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCAGGAACAAGGCGTTGAGCTTCTTGCCGATA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 14.00% | 0.10% | 34.41% | 51.40% | NA |
| All Indica | 2759 | 2.50% | 0.20% | 49.55% | 47.77% | NA |
| All Japonica | 1512 | 38.00% | 0.00% | 4.10% | 57.94% | NA |
| Aus | 269 | 1.50% | 0.40% | 55.39% | 42.75% | NA |
| Indica I | 595 | 2.40% | 0.00% | 27.90% | 69.75% | NA |
| Indica II | 465 | 4.30% | 0.20% | 48.60% | 46.88% | NA |
| Indica III | 913 | 1.50% | 0.30% | 70.87% | 27.27% | NA |
| Indica Intermediate | 786 | 2.50% | 0.30% | 41.73% | 55.47% | NA |
| Temperate Japonica | 767 | 63.20% | 0.00% | 0.00% | 36.77% | NA |
| Tropical Japonica | 504 | 7.10% | 0.00% | 8.73% | 84.13% | NA |
| Japonica Intermediate | 241 | 22.00% | 0.00% | 7.47% | 70.54% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 23.96% | 75.00% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 27.78% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654182 | T -> C | LOC_Os04g51730.1 | synonymous_variant ; p.Lys60Lys; LOW | synonymous_codon | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |
| vg0430654182 | T -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |