Variant ID: vg0324794178 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 24794178 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTGTCAACATCAACATAAACCTGTGATAGAGGTTGCTGGGCTCGTCGATCGGACAAATTGCGTTGATTTGTCATGGTCATCTGAGAAGAGCCTTTCGAT[G/A]
GCATTGCTTTCCTAACCCCCAAAAAAAAGAAAGAAAAAAGAAATACACAATCCTTATCAGAGAGGGATTTACACCTACAGTGCCAATGAAACAAACTAGT
ACTAGTTTGTTTCATTGGCACTGTAGGTGTAAATCCCTCTCTGATAAGGATTGTGTATTTCTTTTTTCTTTCTTTTTTTTGGGGGTTAGGAAAGCAATGC[C/T]
ATCGAAAGGCTCTTCTCAGATGACCATGACAAATCAACGCAATTTGTCCGATCGACGAGCCCAGCAACCTCTATCACAGGTTTATGTTGATGTTGACAGT
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 | 65.00% | 0.20% | 8.89% | 25.88% | NA |
All Indica | 2759 | 48.10% | 0.10% | 8.92% | 42.88% | NA |
All Japonica | 1512 | 99.40% | 0.00% | 0.13% | 0.46% | NA |
Aus | 269 | 34.90% | 1.90% | 57.62% | 5.58% | NA |
Indica I | 595 | 78.20% | 0.00% | 5.04% | 16.81% | NA |
Indica II | 465 | 20.40% | 0.00% | 6.45% | 73.12% | NA |
Indica III | 913 | 35.50% | 0.40% | 15.12% | 48.96% | NA |
Indica Intermediate | 786 | 56.20% | 0.00% | 6.11% | 37.66% | NA |
Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 92.70% | 0.00% | 5.21% | 2.08% | NA |
Intermediate | 90 | 68.90% | 0.00% | 13.33% | 17.78% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0324794178 | G -> A | LOC_Os03g44130.1 | missense_variant ; p.Pro2Leu; MODERATE | nonsynonymous_codon ; P2L | Average:10.907; most accessible tissue: Zhenshan97 flower, score: 32.793 | unknown | unknown | DELETERIOUS | 0.02 |
vg0324794178 | G -> DEL | LOC_Os03g44130.1 | N | frameshift_variant | Average:10.907; most accessible tissue: Zhenshan97 flower, score: 32.793 | N | N | N | N |