Variant ID: vg1218481396 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 18481396 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGTCACCGTG[A/C]
AGGCCGAACCGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCGCAGCAGTGA
TCACTGCTGCGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACGGTTCGGCCT[T/G]
CACGGTGACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGG
Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 13.10% | 0.30% | 2.92% | 83.66% | NA |
All Indica | 2759 | 2.10% | 0.50% | 3.26% | 94.06% | NA |
All Japonica | 1512 | 35.10% | 0.00% | 0.46% | 64.48% | NA |
Aus | 269 | 1.50% | 0.00% | 13.75% | 84.76% | NA |
Indica I | 595 | 3.20% | 0.00% | 2.18% | 94.62% | NA |
Indica II | 465 | 3.00% | 0.00% | 3.01% | 93.98% | NA |
Indica III | 913 | 0.30% | 1.60% | 3.07% | 94.96% | NA |
Indica Intermediate | 786 | 2.90% | 0.00% | 4.45% | 92.62% | NA |
Temperate Japonica | 767 | 59.60% | 0.00% | 0.26% | 40.16% | NA |
Tropical Japonica | 504 | 3.00% | 0.00% | 0.40% | 96.63% | NA |
Japonica Intermediate | 241 | 24.10% | 0.00% | 1.24% | 74.69% | NA |
VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
Intermediate | 90 | 27.80% | 1.10% | 3.33% | 67.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1218481396 | A -> C | LOC_Os12g30780.1 | synonymous_variant ; p.Leu47Leu; LOW | nonsynonymous_codon ; L47P | Average:23.895; most accessible tissue: Minghui63 young leaf, score: 42.042 | unknown | unknown | DELETERIOUS | 0.02 |
vg1218481396 | A -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:23.895; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |