| Variant ID: vg0811599950 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599950 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGAAGAAAAACCAAAAGACAAAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATGAATACGGCCGCGGTGGGCGCGGGGACGAACCTGC[G/A]
GGGAGGTCGGCTAAACGACCACCTCGGGGGTGAGATGAGGTTCCCCCGGCATGGCACAATCCCCCCCATCTTGCGGGGCCGTTTCTTCTTTCGCTCCCCC
GGGGGAGCGAAAGAAGAAACGGCCCCGCAAGATGGGGGGGATTGTGCCATGCCGGGGGAACCTCATCTCACCCCCGAGGTGGTCGTTTAGCCGACCTCCC[C/T]
GCAGGTTCGTCCCCGCGCCCACCGCGGCCGTATTCATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTTTGTCTTTTGGTTTTTCTTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.30% | 0.90% | 2.71% | 94.12% | NA |
| All Indica | 2759 | 0.10% | 1.40% | 4.24% | 94.16% | NA |
| All Japonica | 1512 | 6.80% | 0.00% | 0.53% | 92.66% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.12% | 98.88% | NA |
| Indica I | 595 | 0.00% | 0.50% | 1.18% | 98.32% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.20% | 3.00% | 9.97% | 86.86% | NA |
| Indica Intermediate | 786 | 0.30% | 1.30% | 2.04% | 96.44% | NA |
| Temperate Japonica | 767 | 8.70% | 0.00% | 0.78% | 90.48% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 0.00% | 95.24% | NA |
| Japonica Intermediate | 241 | 5.00% | 0.00% | 0.83% | 94.19% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 2.20% | 1.10% | 0.00% | 96.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599950 | G -> A | LOC_Os08g19380.1 | upstream_gene_variant ; 4027.0bp to feature; MODIFIER | silent_mutation | Average:11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599950 | G -> A | LOC_Os08g19410.1 | upstream_gene_variant ; 3283.0bp to feature; MODIFIER | silent_mutation | Average:11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599950 | G -> A | LOC_Os08g19390.1 | downstream_gene_variant ; 1675.0bp to feature; MODIFIER | silent_mutation | Average:11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599950 | G -> A | LOC_Os08g19400.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599950 | G -> DEL | N | N | silent_mutation | Average:11.514; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |