| Variant ID: vg1023166777 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166777 |
| Reference Allele: T | Alternative Allele: G,C |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTATAAACAATAACAAAACTCTGTTATTTACTCTCTGTAAAATTCTCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTC[T/G,C]
ATTGTAATTTGCATGAAAATATACAAAATACATGTTCAGAAGCATTTCTCACATTTATCTATTCTCTAAACAATTTTCACGTTGGTTCAAATTGCTTAGA
TCTAAGCAATTTGAACCAACGTGAAAATTGTTTAGAGAATAGATAAATGTGAGAAATGCTTCTGAACATGTATTTTGTATATTTTCATGCAAATTACAAT[A/C,G]
GAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGAGAATTTTACAGAGAGTAAATAACAGAGTTTTGTTATTGTTTATAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.90% | 2.70% | 5.01% | 12.42% | C: 0.91% |
| All Indica | 2759 | 65.90% | 4.50% | 8.34% | 20.01% | C: 1.23% |
| All Japonica | 1512 | 99.60% | 0.10% | 0.07% | 0.26% | NA |
| Aus | 269 | 87.40% | 0.00% | 1.49% | 8.18% | C: 2.97% |
| Indica I | 595 | 44.50% | 7.10% | 11.93% | 36.47% | NA |
| Indica II | 465 | 57.60% | 4.70% | 9.68% | 27.74% | C: 0.22% |
| Indica III | 913 | 83.70% | 2.70% | 5.04% | 5.26% | C: 3.29% |
| Indica Intermediate | 786 | 66.40% | 4.50% | 8.65% | 20.10% | C: 0.38% |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 2.22% | 8.89% | C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166777 | T -> C | LOC_Os10g42970.1 | upstream_gene_variant ; 4362.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> C | LOC_Os10g42999.1 | upstream_gene_variant ; 2676.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> C | LOC_Os10g42970.2 | upstream_gene_variant ; 4362.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> C | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> G | LOC_Os10g42970.1 | upstream_gene_variant ; 4362.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> G | LOC_Os10g42999.1 | upstream_gene_variant ; 2676.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> G | LOC_Os10g42970.2 | upstream_gene_variant ; 4362.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> G | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166777 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |