| Variant ID: vg0508168782 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8168782 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CATCTCCTCCTCAGGATCCTGCACCGTCTCCTCCTCATGCTCCGCCAGCACCGTCTCCACCTCAGGCTCCAGCATCGACTCCTCCTCAGGATCCTGCACC[G/A]
ACTCCTCCTCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGGCCCCCCCAGCTCCACCGCCTGCCCACACAAGGG
CCCTTGTGTGGGCAGGCGGTGGAGCTGGGGGGGCCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGAGGAGGAGT[C/T]
GGTGCAGGATCCTGAGGAGGAGTCGATGCTGGAGCCTGAGGTGGAGACGGTGCTGGCGGAGCATGAGGAGGAGACGGTGCAGGATCCTGAGGAGGAGATG
| 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 | 26.60% | 0.60% | 25.86% | 47.00% | NA |
| All Indica | 2759 | 16.90% | 0.00% | 24.50% | 58.57% | NA |
| All Japonica | 1512 | 42.80% | 1.80% | 28.57% | 26.85% | NA |
| Aus | 269 | 15.60% | 0.00% | 27.51% | 56.88% | NA |
| Indica I | 595 | 12.80% | 0.00% | 19.66% | 67.56% | NA |
| Indica II | 465 | 20.40% | 0.00% | 22.80% | 56.77% | NA |
| Indica III | 913 | 14.10% | 0.00% | 34.17% | 51.70% | NA |
| Indica Intermediate | 786 | 21.10% | 0.10% | 17.94% | 60.81% | NA |
| Temperate Japonica | 767 | 31.80% | 3.50% | 36.51% | 28.16% | NA |
| Tropical Japonica | 504 | 60.50% | 0.00% | 18.45% | 21.03% | NA |
| Japonica Intermediate | 241 | 40.70% | 0.00% | 24.48% | 34.85% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 20.83% | 15.62% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 22.22% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508168782 | G -> DEL | LOC_Os05g14460.1 | N | frameshift_variant | Average:9.572; most accessible tissue: Zhenshan97 root, score: 15.132 | N | N | N | N |
| vg0508168782 | G -> A | LOC_Os05g14460.1 | synonymous_variant ; p.Pro592Pro; LOW | synonymous_codon | Average:9.572; most accessible tissue: Zhenshan97 root, score: 15.132 | N | N | N | N |