| Variant ID: vg1023166702 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166702 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTCGAAATTTAATTTTAGAAACACTAATTTTCATCAATTTCATCTATTTGCAGCGGAAGATCTATATACAATTCGTATAAACAATAACAAAACTCTGTT[A/G]
TTTACTCTCTGTAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTCTATTGTAATTTGCATGAAAATATACA
TGTATATTTTCATGCAAATTACAATAGAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGAGAATTTTACAGAGAGTAAA[T/C]
AACAGAGTTTTGTTATTGTTTATACGAATTGTATATAGATCTTCCGCTGCAAATAGATGAAATTGATGAAAATTAGTGTTTCTAAAATTAAATTTCGAAC
| 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 | 23.00% | 1.00% | 29.48% | 46.55% | NA |
| All Indica | 2759 | 2.10% | 1.70% | 31.10% | 65.10% | NA |
| All Japonica | 1512 | 65.70% | 0.00% | 26.52% | 7.80% | NA |
| Aus | 269 | 0.40% | 0.40% | 16.73% | 82.53% | NA |
| Indica I | 595 | 3.90% | 0.50% | 12.44% | 83.19% | NA |
| Indica II | 465 | 1.90% | 0.40% | 9.46% | 88.17% | NA |
| Indica III | 913 | 0.20% | 3.40% | 56.52% | 39.87% | NA |
| Indica Intermediate | 786 | 3.20% | 1.30% | 28.50% | 67.05% | NA |
| Temperate Japonica | 767 | 94.00% | 0.00% | 3.00% | 3.00% | NA |
| Tropical Japonica | 504 | 33.10% | 0.00% | 55.56% | 11.31% | NA |
| Japonica Intermediate | 241 | 43.60% | 0.00% | 40.66% | 15.77% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 60.42% | 28.12% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 34.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166702 | A -> G | LOC_Os10g42970.1 | upstream_gene_variant ; 4287.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166702 | A -> G | LOC_Os10g42999.1 | upstream_gene_variant ; 2751.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166702 | A -> G | LOC_Os10g42970.2 | upstream_gene_variant ; 4287.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166702 | 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 |
| vg1023166702 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |