| Variant ID: vg1126363195 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26363195 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGCTCACGTTTCTCGCCGGAGTTTCAAGGCCATGAGGCGAGAGCTTCTCGCCGCGGCCCCTACTCATGAGGCGACGCGTCGGGCGCGGTGGTCGGAGGT[G/T]
GCCCTCACCTTTGACCAGACCGACCACCCACCGTGCGTTGCCCGGGGAGGGCAGATTGAGATGGTGGTTTCCCCCACCATCTGCAATGTGAAGTTGGGGC
GCCCCAACTTCACATTGCAGATGGTGGGGGAAACCACCATCTCAATCTGCCCTCCCCGGGCAACGCACGGTGGGTGGTCGGTCTGGTCAAAGGTGAGGGC[C/A]
ACCTCCGACCACCGCGCCCGACGCGTCGCCTCATGAGTAGGGGCCGCGGCGAGAAGCTCTCGCCTCATGGCCTTGAAACTCCGGCGAGAAACGTGAGCAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.50% | 0.10% | 23.99% | 69.42% | NA |
| All Indica | 2759 | 1.10% | 0.20% | 20.26% | 78.47% | NA |
| All Japonica | 1512 | 17.60% | 0.00% | 28.90% | 53.51% | NA |
| Aus | 269 | 0.00% | 0.00% | 34.94% | 65.06% | NA |
| Indica I | 595 | 1.20% | 0.00% | 9.75% | 89.08% | NA |
| Indica II | 465 | 2.20% | 0.00% | 4.95% | 92.90% | NA |
| Indica III | 913 | 0.10% | 0.40% | 35.60% | 63.86% | NA |
| Indica Intermediate | 786 | 1.50% | 0.10% | 19.47% | 78.88% | NA |
| Temperate Japonica | 767 | 30.20% | 0.00% | 18.90% | 50.85% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 41.67% | 57.34% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.00% | 34.02% | 53.94% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 21.88% | 78.12% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 25.56% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126363195 | G -> T | LOC_Os11g43670.1 | synonymous_variant ; p.Val592Val; LOW | synonymous_codon | Average:7.299; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1126363195 | G -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:7.299; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |