| Variant ID: vg1023166805 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166805 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TACTCTCTGTAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTCTATTGTAATTTGCATGAAAATATACAAA[A/G]
TACATGTTCAGAAGCATTTCTCACATTTATCTATTCTCTAAACAATTTTCACGTTGGTTCAAATTGCTTAGAAATAATCACAATAATTATACATAATTGA
TCAATTATGTATAATTATTGTGATTATTTCTAAGCAATTTGAACCAACGTGAAAATTGTTTAGAGAATAGATAAATGTGAGAAATGCTTCTGAACATGTA[T/C]
TTTGTATATTTTCATGCAAATTACAATAGAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGAGAATTTTACAGAGAGTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.20% | 9.20% | 56.77% | 3.81% | NA |
| All Indica | 2759 | 10.30% | 12.60% | 72.78% | 4.24% | NA |
| All Japonica | 1512 | 66.00% | 0.50% | 29.89% | 3.57% | NA |
| Aus | 269 | 9.30% | 28.30% | 61.34% | 1.12% | NA |
| Indica I | 595 | 2.90% | 6.70% | 81.68% | 8.74% | NA |
| Indica II | 465 | 4.90% | 17.00% | 72.04% | 6.02% | NA |
| Indica III | 913 | 20.40% | 13.00% | 66.16% | 0.44% | NA |
| Indica Intermediate | 786 | 7.50% | 14.10% | 74.17% | 4.20% | NA |
| Temperate Japonica | 767 | 43.00% | 0.40% | 50.46% | 6.13% | NA |
| Tropical Japonica | 504 | 93.80% | 0.80% | 4.76% | 0.60% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 17.01% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 13.54% | 0.00% | NA |
| Intermediate | 90 | 41.10% | 2.20% | 50.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166805 | A -> G | LOC_Os10g42970.1 | upstream_gene_variant ; 4390.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166805 | A -> G | LOC_Os10g42999.1 | upstream_gene_variant ; 2648.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166805 | A -> G | LOC_Os10g42970.2 | upstream_gene_variant ; 4390.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166805 | A -> G | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166805 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |