| Variant ID: vg0817015857 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015857 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTG[T/C]
TTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACAT
ATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAA[A/G]
CAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTT
| 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 | 32.20% | 0.10% | 18.94% | 48.71% | NA |
| All Indica | 2759 | 15.60% | 0.10% | 24.94% | 59.33% | NA |
| All Japonica | 1512 | 63.20% | 0.10% | 3.97% | 32.80% | NA |
| Aus | 269 | 23.00% | 0.00% | 36.06% | 40.89% | NA |
| Indica I | 595 | 8.60% | 0.00% | 11.26% | 80.17% | NA |
| Indica II | 465 | 4.30% | 0.00% | 26.02% | 69.68% | NA |
| Indica III | 913 | 26.70% | 0.30% | 33.52% | 39.43% | NA |
| Indica Intermediate | 786 | 14.80% | 0.00% | 24.68% | 60.56% | NA |
| Temperate Japonica | 767 | 79.80% | 0.00% | 1.17% | 19.04% | NA |
| Tropical Japonica | 504 | 36.70% | 0.20% | 8.53% | 54.56% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 3.32% | 31.12% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 39.58% | 20.83% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 13.33% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015857 | T -> C | LOC_Os08g27910.1 | missense_variant ; p.Val422Ala; MODERATE | nonsynonymous_codon ; V422A | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0817015857 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |