| Variant ID: vg1221991830 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21991830 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCTACATACCAAATTTCATTCCCGTACGAACTTGCTAAGTGTTTCATATGTAATGCATCCCACGCACATTGCAGATTCCACTAGGTGCTTTTATTCATC[G/A]
ACCTGGAGGCCTGCACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACATTTGACAAGGTTTTCGAACTTATAGACAGGTACCGTCATAAGTT
AACTTATGACGGTACCTGTCTATAAGTTCGAAAACCTTGTCAAATGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGTGCAGGCCTCCAGGT[C/T]
GATGAATAAAAGCACCTAGTGGAATCTGCAATGTGCGTGGGATGCATTACATATGAAACACTTAGCAAGTTCGTACGGGAATGAAATTTGGTATGTAGGA
| 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 | 66.50% | 0.10% | 2.71% | 30.64% | NA |
| All Indica | 2759 | 54.30% | 0.00% | 2.90% | 42.77% | NA |
| All Japonica | 1512 | 90.50% | 0.30% | 0.53% | 8.60% | NA |
| Aus | 269 | 45.40% | 0.00% | 8.18% | 46.47% | NA |
| Indica I | 595 | 68.10% | 0.00% | 1.01% | 30.92% | NA |
| Indica II | 465 | 72.30% | 0.00% | 0.86% | 26.88% | NA |
| Indica III | 913 | 33.40% | 0.00% | 5.91% | 60.68% | NA |
| Indica Intermediate | 786 | 57.60% | 0.00% | 2.04% | 40.33% | NA |
| Temperate Japonica | 767 | 95.40% | 0.70% | 0.39% | 3.52% | NA |
| Tropical Japonica | 504 | 80.20% | 0.00% | 0.40% | 19.44% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 1.24% | 2.07% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 2.22% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221991830 | G -> DEL | N | N | silent_mutation | Average:10.414; most accessible tissue: Minghui63 flower, score: 20.805 | N | N | N | N |
| vg1221991830 | G -> A | LOC_Os12g35980.1 | upstream_gene_variant ; 3250.0bp to feature; MODIFIER | silent_mutation | Average:10.414; most accessible tissue: Minghui63 flower, score: 20.805 | N | N | N | N |
| vg1221991830 | G -> A | LOC_Os12g35970.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.414; most accessible tissue: Minghui63 flower, score: 20.805 | N | N | N | N |