| Variant ID: vg1023166781 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166781 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAACAATAACAAAACTCTGTTATTTACTCTCTGTAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTCTATT[G/A]
TAATTTGCATGAAAATATACAAAATACATGTTCAGAAGCATTTCTCACATTTATCTATTCTCTAAACAATTTTCACGTTGGTTCAAATTGCTTAGAAATA
TATTTCTAAGCAATTTGAACCAACGTGAAAATTGTTTAGAGAATAGATAAATGTGAGAAATGCTTCTGAACATGTATTTTGTATATTTTCATGCAAATTA[C/T]
AATAGAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGAGAATTTTACAGAGAGTAAATAACAGAGTTTTGTTATTGTTT
| 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 | 77.50% | 2.00% | 7.89% | 12.67% | NA |
| All Indica | 2759 | 63.30% | 3.20% | 13.01% | 20.44% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.13% | 0.26% | NA |
| Aus | 269 | 89.20% | 0.00% | 2.60% | 8.18% | NA |
| Indica I | 595 | 49.70% | 1.00% | 10.92% | 38.32% | NA |
| Indica II | 465 | 68.60% | 0.40% | 3.23% | 27.74% | NA |
| Indica III | 913 | 67.10% | 7.20% | 20.37% | 5.26% | NA |
| Indica Intermediate | 786 | 66.00% | 1.90% | 11.83% | 20.23% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 82.20% | 3.30% | 5.56% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166781 | G -> A | LOC_Os10g42970.1 | upstream_gene_variant ; 4366.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166781 | G -> A | LOC_Os10g42999.1 | upstream_gene_variant ; 2672.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166781 | G -> A | LOC_Os10g42970.2 | upstream_gene_variant ; 4366.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166781 | G -> A | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166781 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |