| Variant ID: vg0131448594 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31448594 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACGCCCCAACTTCACGTTGCAAACGGTGGGAGAAACCACCATCGCAATCTGCCCTCCCCGGGCAACGCACGGTGGGTGGTCGGTCTGGTCGAAGGTGAG[G/A]
GCAACCTCCGACCACCGCGCCCGGCGCGTCGCCTCATGAGTAGGGGCCGTGGCCAGAAGCTCTCGCTTCATGGCCTTGAAGCTCCGGCGAGAAACGTGAG
CTCACGTTTCTCGCCGGAGCTTCAAGGCCATGAAGCGAGAGCTTCTGGCCACGGCCCCTACTCATGAGGCGACGCGCCGGGCGCGGTGGTCGGAGGTTGC[C/T]
CTCACCTTCGACCAGACCGACCACCCACCGTGCGTTGCCCGGGGAGGGCAGATTGCGATGGTGGTTTCTCCCACCGTTTGCAACGTGAAGTTGGGGCGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.00% | 0.60% | 8.59% | 43.91% | NA |
| All Indica | 2759 | 28.40% | 0.90% | 14.10% | 56.54% | NA |
| All Japonica | 1512 | 83.50% | 0.00% | 0.26% | 16.20% | NA |
| Aus | 269 | 4.80% | 0.00% | 2.97% | 92.19% | NA |
| Indica I | 595 | 20.00% | 1.50% | 15.29% | 63.19% | NA |
| Indica II | 465 | 19.60% | 0.60% | 9.25% | 70.54% | NA |
| Indica III | 913 | 37.60% | 0.10% | 15.77% | 46.55% | NA |
| Indica Intermediate | 786 | 29.40% | 1.70% | 14.12% | 54.83% | NA |
| Temperate Japonica | 767 | 88.10% | 0.00% | 0.00% | 11.86% | NA |
| Tropical Japonica | 504 | 90.50% | 0.00% | 0.79% | 8.73% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 0.00% | 45.64% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 4.44% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131448594 | G -> A | LOC_Os01g54660.1 | synonymous_variant ; p.Ala593Ala; LOW | synonymous_codon | Average:21.181; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0131448594 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:21.181; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |