| Variant ID: vg0112723152 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723152 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAGAAGTGGCCAATGTGGGAACAAAGTCGTCCATCAATAACAATGAAGACACCAGTCGGCGGCGACGAAGGCGGTCGACGGTGAAAGCGAAGATGCCCAC[T/C]
AATGGCGGCATAATAGGTCAGCCGTGTAAGCGGAAACACCAGTCGACGGCAACGAAGGTGAGCCAACGGTGACGATGTAGACATCCAACAACGGCGGCAT
ATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTTGGCTCACCTTCGTTGCCGTCGACTGGTGTTTCCGCTTACACGGCTGACCTATTATGCCGCCATT[A/G]
GTGGGCATCTTCGCTTTCACCGTCGACCGCCTTCGTCGCCGCCGACTGGTGTCTTCATTGTTATTGATGGACGACTTTGTTCCCACATTGGCCACTTCTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.70% | 0.20% | 20.29% | 32.84% | NA |
| All Indica | 2759 | 18.10% | 0.30% | 31.06% | 50.63% | NA |
| All Japonica | 1512 | 96.00% | 0.00% | 2.45% | 1.59% | NA |
| Aus | 269 | 49.80% | 0.00% | 9.67% | 40.52% | NA |
| Indica I | 595 | 4.50% | 0.00% | 14.62% | 80.84% | NA |
| Indica II | 465 | 16.60% | 0.00% | 36.13% | 47.31% | NA |
| Indica III | 913 | 25.70% | 0.70% | 43.04% | 30.56% | NA |
| Indica Intermediate | 786 | 20.20% | 0.10% | 26.59% | 53.05% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.91% | 0.78% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 5.16% | 2.78% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 1.66% | 1.66% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 29.17% | 4.17% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 12.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723152 | T -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.389; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |
| vg0112723152 | T -> C | LOC_Os01g22620.1 | stop_lost&splice_region_variant ; p.Ter426Trpext*?; HIGH | stop_lost | Average:16.389; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 | N | N | N | N |