| Variant ID: vg0315011458 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011458 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACGCGCGACGCCGTCTTCGACGCCGAGGACGCCCTCGATCATTTCTATCTCCGCGTCGATATGTCCAGGTATATATAGCTGCTACTAGATACTCCCTC[T/C]
ATTTTTTAATAGACGACGCCGTTGACTTTTTCTTCCATATTTGACTATTCGTCTTATTCAAAAAATTTTATGTAAATATATAAAATATAAATCACACTTA
TAAGTGTGATTTATATTTTATATATTTACATAAAATTTTTTGAATAAGACGAATAGTCAAATATGGAAGAAAAAGTCAACGGCGTCGTCTATTAAAAAAT[A/G]
GAGGGAGTATCTAGTAGCAGCTATATATACCTGGACATATCGACGCGGAGATAGAAATGATCGAGGGCGTCCTCGGCGTCGAAGACGGCGTCGCGCGTCT
| 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 | 92.70% | 5.90% | 1.40% | 0.00% | NA |
| All Indica | 2759 | 93.00% | 4.80% | 2.17% | 0.00% | NA |
| All Japonica | 1512 | 90.20% | 9.50% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.00% | 0.00% | 3.03% | 0.00% | NA |
| Indica II | 465 | 96.10% | 1.50% | 2.37% | 0.00% | NA |
| Indica III | 913 | 87.80% | 11.80% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 2.30% | 3.56% | 0.00% | NA |
| Temperate Japonica | 767 | 93.00% | 7.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.80% | 3.40% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 69.70% | 29.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011458 | T -> C | LOC_Os03g26240.1 | upstream_gene_variant ; 2005.0bp to feature; MODIFIER | silent_mutation | Average:61.981; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011458 | T -> C | LOC_Os03g26260.1 | upstream_gene_variant ; 4348.0bp to feature; MODIFIER | silent_mutation | Average:61.981; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011458 | T -> C | LOC_Os03g26229.1 | downstream_gene_variant ; 3198.0bp to feature; MODIFIER | silent_mutation | Average:61.981; most accessible tissue: Callus, score: 78.971 | N | N | N | N |
| vg0315011458 | T -> C | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.981; most accessible tissue: Callus, score: 78.971 | N | N | N | N |