Variant ID: vg0804462517 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 4462517 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGTAATAAGCCATCAGCAGGAGAGAGGCGAGGGCCTCATCAAGGGGATCATTCGCAAGCTGAAGAAGCTGAGAGCTCGCCATGAGATTGCCAACCAGAT[C/T]
GAGGCACTCAAGGCCCATGTCGTCGAGGAGAGCAAGCGACACAAGAGGTATGATCTTCTCAAGCCATGGTCCAGCAGCTCTGCCACTTTTACTATCGACC
GGTCGATAGTAAAAGTGGCAGAGCTGCTGGACCATGGCTTGAGAAGATCATACCTCTTGTGTCGCTTGCTCTCCTCGACGACATGGGCCTTGAGTGCCTC[G/A]
ATCTGGTTGGCAATCTCATGGCGAGCTCTCAGCTTCTTCAGCTTGCGAATGATCCCCTTGATGAGGCCCTCGCCTCTCTCCTGCTGATGGCTTATTACAC
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 33.90% | 0.90% | 1.67% | 63.52% | NA |
All Indica | 2759 | 5.80% | 0.00% | 1.16% | 93.04% | NA |
All Japonica | 1512 | 91.20% | 2.90% | 1.12% | 4.76% | NA |
Aus | 269 | 3.70% | 0.00% | 7.06% | 89.22% | NA |
Indica I | 595 | 8.10% | 0.00% | 1.51% | 90.42% | NA |
Indica II | 465 | 8.40% | 0.00% | 1.08% | 90.54% | NA |
Indica III | 913 | 2.70% | 0.00% | 0.55% | 96.71% | NA |
Indica Intermediate | 786 | 6.10% | 0.00% | 1.65% | 92.24% | NA |
Temperate Japonica | 767 | 91.80% | 5.00% | 1.69% | 1.56% | NA |
Tropical Japonica | 504 | 88.30% | 0.40% | 0.60% | 10.71% | NA |
Japonica Intermediate | 241 | 95.40% | 1.70% | 0.41% | 2.49% | NA |
VI/Aromatic | 96 | 14.60% | 0.00% | 8.33% | 77.08% | NA |
Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0804462517 | C -> T | LOC_Os08g07920.1 | synonymous_variant ; p.Ile123Ile; LOW | synonymous_codon | Average:12.914; most accessible tissue: Callus, score: 76.262 | N | N | N | N |
vg0804462517 | C -> DEL | LOC_Os08g07920.1 | N | frameshift_variant | Average:12.914; most accessible tissue: Callus, score: 76.262 | N | N | N | N |