| Variant ID: vg1023166721 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166721 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAACACTAATTTTCATCAATTTCATCTATTTGCAGCGGAAGATCTATATACAATTCGTATAAACAATAACAAAACTCTGTTATTTACTCTCTGTAAAATT[C/T]
TCCCGTTGGTTCAAATTTAAACAGAGGTAAAACATGCAAAAACAATTCAAAATTCTATTGTAATTTGCATGAAAATATACAAAATACATGTTCAGAAGCA
TGCTTCTGAACATGTATTTTGTATATTTTCATGCAAATTACAATAGAATTTTGAATTGTTTTTGCATGTTTTACCTCTGTTTAAATTTGAACCAACGGGA[G/A]
AATTTTACAGAGAGTAAATAACAGAGTTTTGTTATTGTTTATACGAATTGTATATAGATCTTCCGCTGCAAATAGATGAAATTGATGAAAATTAGTGTTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.30% | 4.10% | 17.50% | 13.12% | NA |
| All Indica | 2759 | 51.60% | 5.70% | 21.53% | 21.13% | NA |
| All Japonica | 1512 | 96.00% | 0.10% | 3.51% | 0.33% | NA |
| Aus | 269 | 21.20% | 10.00% | 60.22% | 8.55% | NA |
| Indica I | 595 | 33.10% | 5.20% | 25.55% | 36.13% | NA |
| Indica II | 465 | 37.00% | 5.60% | 27.10% | 30.32% | NA |
| Indica III | 913 | 74.70% | 5.70% | 14.24% | 5.37% | NA |
| Indica Intermediate | 786 | 47.60% | 6.10% | 23.66% | 22.65% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 89.10% | 0.20% | 10.12% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 2.10% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 4.40% | 13.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166721 | C -> T | LOC_Os10g42970.1 | upstream_gene_variant ; 4306.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166721 | C -> T | LOC_Os10g42999.1 | upstream_gene_variant ; 2732.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166721 | C -> T | LOC_Os10g42970.2 | upstream_gene_variant ; 4306.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166721 | C -> T | LOC_Os10g42980.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166721 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |