| Variant ID: vg0817015858 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015858 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGT[T/C]
TGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATT
AATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACA[A/G]
ACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCT
| 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 | 32.10% | 0.10% | 19.00% | 48.77% | NA |
| All Indica | 2759 | 15.50% | 0.10% | 24.97% | 59.41% | NA |
| All Japonica | 1512 | 63.10% | 0.10% | 3.97% | 32.87% | NA |
| Aus | 269 | 22.30% | 0.00% | 36.80% | 40.89% | NA |
| Indica I | 595 | 8.60% | 0.00% | 11.09% | 80.34% | NA |
| Indica II | 465 | 4.30% | 0.00% | 26.24% | 69.46% | NA |
| Indica III | 913 | 26.50% | 0.30% | 33.63% | 39.54% | NA |
| Indica Intermediate | 786 | 14.60% | 0.00% | 24.68% | 60.69% | 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% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015858 | T -> C | LOC_Os08g27910.1 | synonymous_variant ; p.Val422Val; LOW | nonsynonymous_codon ; V422A | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0817015858 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |