Variant ID: vg1105160867 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 5160867 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAATGGGCGGGTGACGTAGGAGCGCGCCC[G/A]
CAGCTTGGAGCGCGCCCTGGGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGT
ACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCCCAGGGCGCGCTCCAAGCTG[C/T]
GGGCGCGCTCCTACGTCACCCGCCCATTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAG
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 | 33.50% | 0.20% | 14.56% | 51.78% | NA |
All Indica | 2759 | 9.90% | 0.30% | 19.06% | 70.71% | NA |
All Japonica | 1512 | 83.80% | 0.00% | 2.65% | 13.56% | NA |
Aus | 269 | 0.70% | 0.00% | 28.25% | 71.00% | NA |
Indica I | 595 | 6.10% | 0.00% | 6.39% | 87.56% | NA |
Indica II | 465 | 5.20% | 1.50% | 14.19% | 79.14% | NA |
Indica III | 913 | 8.20% | 0.00% | 34.06% | 57.72% | NA |
Indica Intermediate | 786 | 17.60% | 0.30% | 14.12% | 68.07% | NA |
Temperate Japonica | 767 | 88.70% | 0.00% | 0.65% | 10.69% | NA |
Tropical Japonica | 504 | 79.00% | 0.00% | 3.57% | 17.46% | NA |
Japonica Intermediate | 241 | 78.40% | 0.00% | 7.05% | 14.52% | NA |
VI/Aromatic | 96 | 9.40% | 0.00% | 36.46% | 54.17% | NA |
Intermediate | 90 | 34.40% | 0.00% | 12.22% | 53.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1105160867 | G -> A | LOC_Os11g09660.1 | missense_variant ; p.Ala85Val; MODERATE | nonsynonymous_codon ; A85V | Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign ![]() |
0.382 ![]() |
TOLERATED | 0.07 |
vg1105160867 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.486; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |