| Variant ID: vg0725421227 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421227 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGACAGGCGGGTGTCGTAGGAGCGCGCCAGCAGCCTGAAGCGCACCCTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCG[T/C]
TCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACCCTCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTAC
GTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGAGGGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGA[A/G]
CGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAGGGTGCGCTTCAGGCTGCTGGCGCGCTCCTACGACACCCGCCTGTCG
| 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 | 24.80% | 0.60% | 1.40% | 73.21% | NA |
| All Indica | 2759 | 5.70% | 0.10% | 1.34% | 92.86% | NA |
| All Japonica | 1512 | 60.30% | 1.60% | 1.19% | 36.97% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 5.00% | 0.00% | 1.01% | 93.95% | NA |
| Indica II | 465 | 3.40% | 0.20% | 0.86% | 95.48% | NA |
| Indica III | 913 | 7.40% | 0.00% | 1.64% | 90.91% | NA |
| Indica Intermediate | 786 | 5.60% | 0.10% | 1.53% | 92.75% | NA |
| Temperate Japonica | 767 | 89.30% | 0.00% | 0.26% | 10.43% | NA |
| Tropical Japonica | 504 | 15.30% | 4.80% | 1.98% | 77.98% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.00% | 2.49% | 35.68% | NA |
| VI/Aromatic | 96 | 70.80% | 0.00% | 2.08% | 27.08% | NA |
| Intermediate | 90 | 33.30% | 1.10% | 6.67% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421227 | T -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421227 | T -> C | LOC_Os07g42460.1 | synonymous_variant ; p.Glu61Glu; LOW | synonymous_codon | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |