| Variant ID: vg0315011702 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011702 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACATGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAAACGGAGGTAGTATGTTATTCCCTTT[T/C]
CTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGACAAATCGGACGTCTGGCATTTCTCAGAACATCGGACGGTGTATTTGTTACAAAATGTTTCA
TGAAACATTTTGTAACAAATACACCGTCCGATGTTCTGAGAAATGCCAGACGTCCGATTTGTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAG[A/G]
AAAGGGAATAACATACTACCTCCGTTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATT
| 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 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011702 | T -> C | LOC_Os03g26240.1 | upstream_gene_variant ; 2249.0bp to feature; MODIFIER | silent_mutation | Average:41.658; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011702 | T -> C | LOC_Os03g26260.1 | upstream_gene_variant ; 4104.0bp to feature; MODIFIER | silent_mutation | Average:41.658; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011702 | T -> C | LOC_Os03g26229.1 | downstream_gene_variant ; 3442.0bp to feature; MODIFIER | silent_mutation | Average:41.658; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011702 | T -> C | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.658; most accessible tissue: Callus, score: 67.433 | N | N | N | N |