| Variant ID: vg0725421179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421179 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGCCACGTCTTCCAGCCATCGTTGGGCTGGAGACTCCGGGTCATGGACGACAGGCGGGTGTCGTAGGAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGG[C/T]
GTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAA
TTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCAC[G/A]
CCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTCCTACGACACCCGCCTGTCGTCCATGACCCGGAGTCTCCAGCCCAACGATGGCTGGAAGACGTGGCCA
| 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 | 25.20% | 0.10% | 3.41% | 71.29% | NA |
| All Indica | 2759 | 5.70% | 0.20% | 3.12% | 91.01% | NA |
| All Japonica | 1512 | 64.20% | 0.10% | 1.12% | 34.59% | NA |
| Aus | 269 | 1.90% | 0.00% | 2.23% | 95.91% | NA |
| Indica I | 595 | 3.90% | 0.30% | 3.03% | 92.77% | NA |
| Indica II | 465 | 3.00% | 0.00% | 2.80% | 94.19% | NA |
| Indica III | 913 | 9.10% | 0.00% | 2.96% | 87.95% | NA |
| Indica Intermediate | 786 | 4.70% | 0.40% | 3.56% | 91.35% | NA |
| Temperate Japonica | 767 | 90.00% | 0.00% | 0.52% | 9.52% | NA |
| Tropical Japonica | 504 | 26.00% | 0.20% | 1.19% | 72.62% | NA |
| Japonica Intermediate | 241 | 62.20% | 0.00% | 2.90% | 34.85% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 50.00% | 25.00% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 4.44% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421179 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:5.012; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg0725421179 | C -> T | LOC_Os07g42460.1 | synonymous_variant ; p.Thr77Thr; LOW | synonymous_codon | Average:5.012; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |