| Variant ID: vg0131447854 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447854 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATGGATGACCTCACGGATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCG[G/A]
ACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTG
CAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGT[C/T]
CGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCATCCATC
| 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 | 40.30% | 3.60% | 18.11% | 37.96% | NA |
| All Indica | 2759 | 23.40% | 6.20% | 29.18% | 41.17% | NA |
| All Japonica | 1512 | 69.40% | 0.00% | 1.52% | 29.10% | NA |
| Aus | 269 | 24.90% | 0.00% | 6.32% | 68.77% | NA |
| Indica I | 595 | 18.80% | 4.00% | 45.71% | 31.43% | NA |
| Indica II | 465 | 18.90% | 3.00% | 13.55% | 64.52% | NA |
| Indica III | 913 | 25.40% | 12.00% | 30.23% | 32.31% | NA |
| Indica Intermediate | 786 | 27.20% | 3.10% | 24.68% | 45.04% | NA |
| Temperate Japonica | 767 | 61.40% | 0.00% | 0.78% | 37.81% | NA |
| Tropical Japonica | 504 | 89.70% | 0.00% | 2.38% | 7.94% | NA |
| Japonica Intermediate | 241 | 52.30% | 0.00% | 2.07% | 45.64% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 12.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447854 | G -> A | LOC_Os01g54660.1 | synonymous_variant ; p.Val827Val; LOW | synonymous_codon | Average:25.293; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg0131447854 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:25.293; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |