| Variant ID: vg0141809260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809260 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGGAGGCCTGCCCCGGGGGCTGGCTCGGAAGTCGGAGGCGCGCTTCGTCGGCGAG[G/A]
GGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCGGTTCAACACCGGCCCCCGCGGTTGGAAGTAGCAGC
GCTGCTACTTCCAACCGCGGGGGCCGGTGTTGAACCGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCC[C/T]
CTCGCCGACGAAGCGCGCCTCCGACTTCCGAGCCAGCCCCCGGGGCAGGCCTCCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCC
| 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 | 27.40% | 0.20% | 4.99% | 67.41% | NA |
| All Indica | 2759 | 17.30% | 0.40% | 6.92% | 75.43% | NA |
| All Japonica | 1512 | 44.60% | 0.00% | 1.32% | 54.10% | NA |
| Aus | 269 | 36.80% | 0.00% | 6.32% | 56.88% | NA |
| Indica I | 595 | 11.30% | 0.30% | 8.40% | 80.00% | NA |
| Indica II | 465 | 11.80% | 0.20% | 3.66% | 84.30% | NA |
| Indica III | 913 | 25.20% | 0.80% | 6.68% | 67.36% | NA |
| Indica Intermediate | 786 | 15.80% | 0.10% | 8.02% | 76.08% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.65% | 22.16% | NA |
| Tropical Japonica | 504 | 6.00% | 0.00% | 1.79% | 92.26% | NA |
| Japonica Intermediate | 241 | 21.60% | 0.00% | 2.49% | 75.93% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 2.08% | 82.29% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 6.67% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809260 | G -> A | LOC_Os01g72070.1 | synonymous_variant ; p.Pro104Pro; LOW | synonymous_codon | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |
| vg0141809260 | G -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |