Variant ID: vg1105159777 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 5159777 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGCTCGAAGGGCCGCGCGCCACCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGCGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGT[G/A]
GCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAG
CTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGC[C/T]
ACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACGCTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGTGGCGCGCGGCCCTTCGAGCC
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 | 40.80% | 0.10% | 25.35% | 33.81% | NA |
All Indica | 2759 | 17.40% | 0.00% | 35.56% | 47.01% | NA |
All Japonica | 1512 | 86.20% | 0.00% | 6.02% | 7.74% | NA |
Aus | 269 | 14.90% | 0.00% | 35.69% | 49.44% | NA |
Indica I | 595 | 14.10% | 0.00% | 16.47% | 69.41% | NA |
Indica II | 465 | 6.50% | 0.00% | 30.75% | 62.80% | NA |
Indica III | 913 | 18.30% | 0.00% | 57.50% | 24.21% | NA |
Indica Intermediate | 786 | 25.40% | 0.00% | 27.35% | 47.20% | NA |
Temperate Japonica | 767 | 90.00% | 0.00% | 1.69% | 8.34% | NA |
Tropical Japonica | 504 | 82.70% | 0.00% | 10.52% | 6.75% | NA |
Japonica Intermediate | 241 | 81.70% | 0.00% | 10.37% | 7.88% | NA |
VI/Aromatic | 96 | 61.50% | 3.10% | 17.71% | 17.71% | NA |
Intermediate | 90 | 47.80% | 0.00% | 14.44% | 37.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1105159777 | G -> A | LOC_Os11g09660.1 | synonymous_variant ; p.Ala448Ala; LOW | synonymous_codon | Average:5.323; most accessible tissue: Callus, score: 10.907 | N | N | N | N |
vg1105159777 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.323; most accessible tissue: Callus, score: 10.907 | N | N | N | N |