| Variant ID: vg0817015873 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015873 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAA[T/A]
GAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATTCCAATCGTATTGTGG
CCACAATACGATTGGAATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTC[A/T]
TTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGA
| 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 | 31.00% | 0.10% | 18.85% | 50.04% | NA |
| All Indica | 2759 | 13.80% | 0.10% | 24.79% | 61.29% | NA |
| All Japonica | 1512 | 63.10% | 0.10% | 3.97% | 32.87% | NA |
| Aus | 269 | 20.10% | 0.00% | 36.43% | 43.49% | NA |
| Indica I | 595 | 7.20% | 0.00% | 9.75% | 83.03% | NA |
| Indica II | 465 | 3.20% | 0.00% | 25.38% | 71.40% | NA |
| Indica III | 913 | 24.80% | 0.30% | 33.95% | 40.96% | NA |
| Indica Intermediate | 786 | 12.30% | 0.00% | 25.19% | 62.47% | NA |
| Temperate Japonica | 767 | 79.80% | 0.00% | 1.17% | 19.04% | NA |
| Tropical Japonica | 504 | 36.50% | 0.20% | 8.73% | 54.56% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 2.90% | 31.54% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 39.58% | 20.83% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 12.22% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015873 | T -> A | LOC_Os08g27910.1 | missense_variant ; p.Asn427Lys; MODERATE | nonsynonymous_codon | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | TOLERATED | 1.00 |
| vg0817015873 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |