Variant ID: vg0101949113 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 1949113 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGATCTCAATGGCCTTCACCTCAGGCTTCTTGACCTCGGCCTTGGGCACGGTGACAGTGAGCACGCCGTTCTCCAGTCCGGCCTTCACCTGGTCCACCTT[G/C]
GCGTTCTCCGGCAGCCTGAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGCGGTGCCACTTGTCGTTCTTGTCCTCCTTCTCCTTGCTGCGCTGGC
GCCAGCGCAGCAAGGAGAAGGAGGACAAGAACGACAAGTGGCACCGCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTCAGGCTGCCGGAGAACGC[C/G]
AAGGTGGACCAGGTGAAGGCCGGACTGGAGAACGGCGTGCTCACTGTCACCGTGCCCAAGGCCGAGGTCAAGAAGCCTGAGGTGAAGGCCATTGAGATCT
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.40% | 5.60% | 3.00% | 0.00% | NA |
All Indica | 2759 | 94.90% | 0.50% | 4.57% | 0.00% | NA |
All Japonica | 1512 | 84.10% | 15.00% | 0.93% | 0.00% | NA |
Aus | 269 | 93.70% | 5.90% | 0.37% | 0.00% | NA |
Indica I | 595 | 81.30% | 1.30% | 17.31% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 96.70% | 0.60% | 2.67% | 0.00% | NA |
Temperate Japonica | 767 | 99.00% | 0.80% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 56.70% | 41.50% | 1.79% | 0.00% | NA |
Japonica Intermediate | 241 | 93.80% | 5.00% | 1.24% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0101949113 | G -> C | LOC_Os01g04370.1 | synonymous_variant ; p.Ala115Ala; LOW | synonymous_codon | Average:68.604; most accessible tissue: Zhenshan97 flower, score: 87.106 | N | N | N | N |