| Variant ID: vg0804463773 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463773 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAATTCCGAGCGAAATCATCGAAATTTCAATCAATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTA[T/C]
TGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTTGAAAATTTATATCCCAATAGGTTCTATGAATATCATACTATTTATAAGATTTTATTTGAT
ATCAAATAAAATCTTATAAATAGTATGATATTCATAGAACCTATTGGGATATAAATTTTCAAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACA[A/G]
TAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTATTGATTGAAATTTCGATGATTTCGCTCGGAATTTC
| 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 | 38.30% | 0.10% | 0.51% | 61.09% | NA |
| All Indica | 2759 | 10.30% | 0.00% | 0.65% | 89.05% | NA |
| All Japonica | 1512 | 95.10% | 0.00% | 0.20% | 4.70% | NA |
| Aus | 269 | 10.80% | 0.00% | 0.74% | 88.48% | NA |
| Indica I | 595 | 17.00% | 0.00% | 1.18% | 81.85% | NA |
| Indica II | 465 | 11.60% | 0.00% | 0.65% | 87.74% | NA |
| Indica III | 913 | 3.20% | 0.00% | 0.11% | 96.71% | NA |
| Indica Intermediate | 786 | 12.60% | 0.10% | 0.89% | 86.39% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.26% | 1.43% | NA |
| Tropical Japonica | 504 | 89.10% | 0.00% | 0.00% | 10.91% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 1.04% | 75.00% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 0.00% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463773 | T -> C | LOC_Os08g07900.1 | upstream_gene_variant ; 3550.0bp to feature; MODIFIER | silent_mutation | Average:14.94; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463773 | T -> C | LOC_Os08g07910.1 | upstream_gene_variant ; 2652.0bp to feature; MODIFIER | silent_mutation | Average:14.94; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463773 | T -> C | LOC_Os08g07930.1 | upstream_gene_variant ; 2256.0bp to feature; MODIFIER | silent_mutation | Average:14.94; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463773 | T -> C | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.94; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463773 | T -> DEL | N | N | silent_mutation | Average:14.94; most accessible tissue: Callus, score: 29.336 | N | N | N | N |