| Variant ID: vg0141809239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809239 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGGAGGCCTGCCCCGGGGGCTGGCTCGGAAGTCG[G/A]
AGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCGGTTCAACACCGGCC
GGCCGGTGTTGAACCGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCT[C/T]
CGACTTCCGAGCCAGCCCCCGGGGCAGGCCTCCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGC
| 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 | 28.20% | 0.20% | 4.63% | 66.99% | NA |
| All Indica | 2759 | 18.40% | 0.30% | 6.45% | 74.81% | NA |
| All Japonica | 1512 | 44.80% | 0.00% | 1.32% | 53.90% | NA |
| Aus | 269 | 37.90% | 0.00% | 5.20% | 56.88% | NA |
| Indica I | 595 | 12.30% | 0.00% | 8.57% | 79.16% | NA |
| Indica II | 465 | 11.80% | 0.20% | 3.44% | 84.52% | NA |
| Indica III | 913 | 26.80% | 0.80% | 6.24% | 66.16% | NA |
| Indica Intermediate | 786 | 17.30% | 0.00% | 6.87% | 75.83% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.65% | 22.16% | NA |
| Tropical Japonica | 504 | 6.20% | 0.00% | 1.98% | 91.87% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.00% | 2.07% | 75.52% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 1.04% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809239 | G -> A | LOC_Os01g72070.1 | synonymous_variant ; p.Leu111Leu; LOW | synonymous_codon | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |
| vg0141809239 | G -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |