Variant ID: vg0106164859 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 6164859 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCTTTCTGAGTATAGCCCTTAGCAACAAGCCGAGCCTTGTACTTTTCAATAGTACCGTCAGGCCTAAGCTTCTTCTTGAACACCCACTTGCACCCCACA[G/A]
GTTTACACCCACCATGCCTTAGGCAGTCCCGCGGTGTCCAACATGGCATTCACCAAGTCAGTCAGTGTGCGGTTCTTCCTTTCAGCAATCCCATTAGACT
AGTCTAATGGGATTGCTGAAAGGAAGAACCGCACACTGACTGACTTGGTGAATGCCATGTTGGACACCGCGGGACTGCCTAAGGCATGGTGGGTGTAAAC[C/T]
TGTGGGGTGCAAGTGGGTGTTCAAGAAGAAGCTTAGGCCTGACGGTACTATTGAAAAGTACAAGGCTCGGCTTGTTGCTAAGGGCTATACTCAGAAAGAA
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 | 22.40% | 0.30% | 14.73% | 62.53% | NA |
All Indica | 2759 | 1.20% | 0.00% | 18.41% | 80.36% | NA |
All Japonica | 1512 | 63.60% | 1.10% | 7.01% | 28.31% | NA |
Aus | 269 | 1.10% | 0.00% | 20.45% | 78.44% | NA |
Indica I | 595 | 0.20% | 0.00% | 6.55% | 93.28% | NA |
Indica II | 465 | 1.30% | 0.00% | 9.89% | 88.82% | NA |
Indica III | 913 | 0.90% | 0.00% | 30.01% | 69.11% | NA |
Indica Intermediate | 786 | 2.40% | 0.00% | 18.96% | 78.63% | NA |
Temperate Japonica | 767 | 92.40% | 2.10% | 1.30% | 4.17% | NA |
Tropical Japonica | 504 | 30.40% | 0.00% | 11.11% | 58.53% | NA |
Japonica Intermediate | 241 | 41.50% | 0.00% | 16.60% | 41.91% | NA |
VI/Aromatic | 96 | 40.60% | 0.00% | 11.46% | 47.92% | NA |
Intermediate | 90 | 23.30% | 0.00% | 17.78% | 58.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0106164859 | G -> A | LOC_Os01g11450.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 | N | N | N | N |
vg0106164859 | G -> DEL | N | N | silent_mutation | Average:4.816; most accessible tissue: Zhenshan97 young leaf, score: 8.295 | N | N | N | N |