| Variant ID: vg0817015841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015841 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAG[T/C]
GTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATT
AATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTAC[A/G]
CTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGG
| 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 | 20.90% | 0.40% | 11.15% | 67.56% | NA |
| All Indica | 2759 | 2.60% | 0.60% | 10.40% | 86.37% | NA |
| All Japonica | 1512 | 56.80% | 0.00% | 7.41% | 35.78% | NA |
| Aus | 269 | 1.10% | 0.70% | 23.42% | 74.72% | NA |
| Indica I | 595 | 4.70% | 0.70% | 1.34% | 93.28% | NA |
| Indica II | 465 | 1.50% | 0.00% | 9.68% | 88.82% | NA |
| Indica III | 913 | 1.80% | 0.70% | 17.42% | 80.18% | NA |
| Indica Intermediate | 786 | 2.80% | 0.80% | 9.54% | 86.90% | NA |
| Temperate Japonica | 767 | 77.70% | 0.00% | 1.43% | 20.86% | NA |
| Tropical Japonica | 504 | 24.20% | 0.00% | 16.07% | 59.72% | NA |
| Japonica Intermediate | 241 | 58.50% | 0.00% | 8.30% | 33.20% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 52.08% | 21.88% | NA |
| Intermediate | 90 | 30.00% | 1.10% | 16.67% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015841 | T -> C | LOC_Os08g27910.1 | missense_variant ; p.Cys417Arg; MODERATE | nonsynonymous_codon ; C417R | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | TOLERATED | 0.33 |
| vg0817015841 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |