| Variant ID: vg0410151816 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10151816 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGTAATAGCAAAAGTAGTACTGCTTTACAAGTTTGTAAGCCAAAAGAAACGGTCACATAAGGACTGAAGAGGTAGAACACTACTGACGAGGCCTCTTAC[C/T]
CCTGTCCCTCCTACCCTGCGCCCTAATGTGCCCGTGGGAGTACGTGAGTCGGTCCGGGGGTACGGCACGGCCAACCCGTCCTGCCTGTACAGGTGTGACC
GGTCACACCTGTACAGGCAGGACGGGTTGGCCGTGCCGTACCCCCGGACCGACTCACGTACTCCCACGGGCACATTAGGGCGCAGGGTAGGAGGGACAGG[G/A]
GTAAGAGGCCTCGTCAGTAGTGTTCTACCTCTTCAGTCCTTATGTGACCGTTTCTTTTGGCTTACAAACTTGTAAAGCAGTACTACTTTTGCTATTACTA
| 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 | 28.80% | 0.00% | 12.23% | 58.97% | NA |
| All Indica | 2759 | 7.10% | 0.00% | 14.90% | 77.96% | NA |
| All Japonica | 1512 | 63.10% | 0.10% | 4.83% | 31.94% | NA |
| Aus | 269 | 49.40% | 0.00% | 20.07% | 30.48% | NA |
| Indica I | 595 | 11.80% | 0.00% | 10.92% | 77.31% | NA |
| Indica II | 465 | 3.40% | 0.00% | 15.05% | 81.51% | NA |
| Indica III | 913 | 2.80% | 0.00% | 16.43% | 80.72% | NA |
| Indica Intermediate | 786 | 10.80% | 0.00% | 16.03% | 73.16% | NA |
| Temperate Japonica | 767 | 95.40% | 0.30% | 1.43% | 2.87% | NA |
| Tropical Japonica | 504 | 9.90% | 0.00% | 11.11% | 78.97% | NA |
| Japonica Intermediate | 241 | 71.40% | 0.00% | 2.49% | 26.14% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 25.00% | 27.08% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 17.78% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410151816 | C -> DEL | LOC_Os04g18390.1 | N | frameshift_variant | Average:5.373; most accessible tissue: Callus, score: 12.42 | N | N | N | N |
| vg0410151816 | C -> T | LOC_Os04g18390.1 | missense_variant ; p.Gly1548Ser; MODERATE | nonsynonymous_codon ; G1548S | Average:5.373; most accessible tissue: Callus, score: 12.42 | unknown | unknown | TOLERATED | 0.28 |