| Variant ID: vg0300825646 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825646 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGAGAGAAGGCGTTACCCTTATTTAAGCTTCTCAAACGCTCCGGACCGTTTACCTGGACGGAGGAAGCCGAAAATGCCCTCACTCAGTTGAAGGCATGT[C/T]
TAAGCTCTCCCCCAGTTCTGGTCGCCCCGGAGCCAGACGAGCCCTTGTTACTCTACTTAGCGGCGACCCCGCAAGTAGTTAGTGCGGCATTGGTTGTGGA
TCCACAACCAATGCCGCACTAACTACTTGCGGGGTCGCCGCTAAGTAGAGTAACAAGGGCTCGTCTGGCTCCGGGGCGACCAGAACTGGGGGAGAGCTTA[G/A]
ACATGCCTTCAACTGAGTGAGGGCATTTTCGGCTTCCTCCGTCCAGGTAAACGGTCCGGAGCGTTTGAGAAGCTTAAATAAGGGTAACGCCTTCTCTCCC
| 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 | 19.10% | 0.50% | 2.22% | 78.10% | NA |
| All Indica | 2759 | 10.80% | 0.70% | 3.15% | 85.36% | NA |
| All Japonica | 1512 | 37.80% | 0.10% | 0.26% | 61.77% | NA |
| Aus | 269 | 3.30% | 0.00% | 0.37% | 96.28% | NA |
| Indica I | 595 | 6.70% | 1.30% | 3.53% | 88.40% | NA |
| Indica II | 465 | 15.70% | 1.50% | 3.01% | 79.78% | NA |
| Indica III | 913 | 10.50% | 0.10% | 1.97% | 87.40% | NA |
| Indica Intermediate | 786 | 11.30% | 0.40% | 4.33% | 83.97% | NA |
| Temperate Japonica | 767 | 61.40% | 0.00% | 0.26% | 38.33% | NA |
| Tropical Japonica | 504 | 6.90% | 0.00% | 0.40% | 92.66% | NA |
| Japonica Intermediate | 241 | 27.40% | 0.80% | 0.00% | 71.78% | NA |
| VI/Aromatic | 96 | 8.30% | 4.20% | 9.38% | 78.12% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 4.44% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825646 | C -> T | LOC_Os03g02350.1 | synonymous_variant ; p.Leu1109Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300825646 | C -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |