| Variant ID: vg1023166961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166961 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGTTCAAATTGCTTAGAAATAATCACAATAATTATACATAATTGAAAAAGCTTCTGAGAGGACCTATTATTAAACTCTTCTTTTCTTTTTCTTTCGGCCC[C/T]
GAGGGACCTAAATTGAACTTTTCCGGCCTTTGCCGGTCGGTCCATGGCCACCTTGCGCACGGGCGAGCGCCCCCTCCCCTCCCCCAGGCCGCAACCTGGG
CCCAGGTTGCGGCCTGGGGGAGGGGAGGGGGCGCTCGCCCGTGCGCAAGGTGGCCATGGACCGACCGGCAAAGGCCGGAAAAGTTCAATTTAGGTCCCTC[G/A]
GGGCCGAAAGAAAAAGAAAAGAAGAGTTTAATAATAGGTCCTCTCAGAAGCTTTTTCAATTATGTATAATTATTGTGATTATTTCTAAGCAATTTGAACC
| 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 | 22.60% | 0.10% | 18.96% | 58.27% | NA |
| All Indica | 2759 | 2.10% | 0.00% | 17.18% | 80.75% | NA |
| All Japonica | 1512 | 64.80% | 0.40% | 22.55% | 12.24% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.12% | 98.88% | NA |
| Indica I | 595 | 3.90% | 0.00% | 3.87% | 92.27% | NA |
| Indica II | 465 | 1.50% | 0.00% | 3.87% | 94.62% | NA |
| Indica III | 913 | 0.30% | 0.00% | 36.04% | 63.64% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 13.23% | 83.72% | NA |
| Temperate Japonica | 767 | 94.00% | 0.00% | 1.69% | 4.30% | NA |
| Tropical Japonica | 504 | 31.50% | 1.00% | 48.61% | 18.85% | NA |
| Japonica Intermediate | 241 | 41.50% | 0.40% | 34.44% | 23.65% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 56.25% | 32.29% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 26.67% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166961 | C -> T | LOC_Os10g42970.1 | upstream_gene_variant ; 4546.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166961 | C -> T | LOC_Os10g42999.1 | upstream_gene_variant ; 2492.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166961 | C -> T | LOC_Os10g42970.2 | upstream_gene_variant ; 4546.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166961 | 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 |
| vg1023166961 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |