| Variant ID: vg1001933837 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933837 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AATACAACAAACTCTTTCACTCTACCTCCATCTGAAGTATTTATGTGTTTTTTGTGCAGCTCTCTAAAAAGCTTGCTTCCCATCTCAGAACAGCCACCCT[T/A]
ATATATAATTAGCTGGAAATGGTTCAGAGCAAAACCAGCAGCCATTTTATCCACAGCTGTTTTCAAGGGATGAGAAAAGTGACTGCAATTTGCCAAGTTT
AAACTTGGCAAATTGCAGTCACTTTTCTCATCCCTTGAAAACAGCTGTGGATAAAATGGCTGCTGGTTTTGCTCTGAACCATTTCCAGCTAATTATATAT[A/T]
AGGGTGGCTGTTCTGAGATGGGAAGCAAGCTTTTTAGAGAGCTGCACAAAAAACACATAAATACTTCAGATGGAGGTAGAGTGAAAGAGTTTGTTGTATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 3.40% | 0.36% | 14.83% | NA |
| All Indica | 2759 | 72.50% | 5.60% | 0.51% | 21.46% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 64.70% | 0.00% | 1.12% | 34.20% | NA |
| Indica I | 595 | 60.30% | 0.00% | 1.34% | 38.32% | NA |
| Indica II | 465 | 82.40% | 3.40% | 0.22% | 13.98% | NA |
| Indica III | 913 | 70.60% | 10.10% | 0.11% | 19.17% | NA |
| Indica Intermediate | 786 | 77.90% | 5.90% | 0.51% | 15.78% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933837 | T -> A | LOC_Os10g04160.1 | stop_gained ; p.Lys16*; HIGH | stop_gained | Average:31.45; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |
| vg1001933837 | T -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:31.45; most accessible tissue: Minghui63 root, score: 66.549 | N | N | N | N |