| Variant ID: vg0141809508 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809508 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGAACAGCCGAAGGGATGGGCGCACCCCGATGAACATTTCGCACAGGTGCGCGAAGATGGCCAATGTCATTACCGCGTTGGGGGTGAGGTGCGCCATCT[G/A]
GAGATCGTAAAACTCCAGAACATCCATGAAGAAAGAAGAAAATGGCGGAACCAGCCCTGCCATTGCAAAAGGGAGGAAGAAGACGGACCGCCCCGGGTAG
CTACCCGGGGCGGTCCGTCTTCTTCCTCCCTTTTGCAATGGCAGGGCTGGTTCCGCCATTTTCTTCTTTCTTCATGGATGTTCTGGAGTTTTACGATCTC[C/T]
AGATGGCGCACCTCACCCCCAACGCGGTAATGACATTGGCCATCTTCGCGCACCTGTGCGAAATGTTCATCGGGGTGCGCCCATCCCTTCGGCTGTTCCG
| 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 | 15.00% | 1.40% | 2.48% | 81.15% | NA |
| All Indica | 2759 | 1.70% | 0.10% | 1.41% | 96.77% | NA |
| All Japonica | 1512 | 35.60% | 4.00% | 4.89% | 55.56% | NA |
| Aus | 269 | 34.60% | 0.00% | 0.37% | 65.06% | NA |
| Indica I | 595 | 2.70% | 0.20% | 4.03% | 93.11% | NA |
| Indica II | 465 | 0.90% | 0.20% | 0.22% | 98.71% | NA |
| Indica III | 913 | 0.20% | 0.00% | 0.99% | 98.80% | NA |
| Indica Intermediate | 786 | 3.20% | 0.10% | 0.64% | 96.06% | NA |
| Temperate Japonica | 767 | 61.70% | 7.20% | 8.74% | 22.43% | NA |
| Tropical Japonica | 504 | 4.60% | 0.00% | 0.40% | 95.04% | NA |
| Japonica Intermediate | 241 | 17.40% | 2.10% | 2.07% | 78.42% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 0.00% | 86.46% | NA |
| Intermediate | 90 | 21.10% | 1.10% | 3.33% | 74.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809508 | G -> A | LOC_Os01g72070.1 | stop_gained ; p.Gln22*; HIGH | stop_gained | Average:5.275; most accessible tissue: Callus, score: 11.339 | N | N | N | N |
| vg0141809508 | G -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:5.275; most accessible tissue: Callus, score: 11.339 | N | N | N | N |