Variant ID: vg0226609469 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 26609469 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, G: 0.47, others allele: 0.00, population size: 111. )
CAAACCAAGCCGTCGGTAGGTCAGAAATGAAACATACTACTGTACATATCAAACCGGAAAATGCGTTGAGCTCACCATAGGCAATGGCGGATCCGACGCC[A/G]
GCGAAGACGAAGAGGAGGGTGGCGATGAACTCCGCCACGTAGGCCTTCACGGACGTGGCGCTGAAGGAGTCACCCAAGCTTCCGAATGCGAGCTTCACCA
TGGTGAAGCTCGCATTCGGAAGCTTGGGTGACTCCTTCAGCGCCACGTCCGTGAAGGCCTACGTGGCGGAGTTCATCGCCACCCTCCTCTTCGTCTTCGC[T/C]
GGCGTCGGATCCGCCATTGCCTATGGTGAGCTCAACGCATTTTCCGGTTTGATATGTACAGTAGTATGTTTCATTTCTGACCTACCGACGGCTTGGTTTG
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 | 60.40% | 39.50% | 0.04% | 0.00% | NA |
All Indica | 2759 | 92.00% | 7.90% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 83.60% | 16.30% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 93.50% | 6.40% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 43.30% | 56.70% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0226609469 | A -> G | LOC_Os02g44080.1 | synonymous_variant ; p.Ala34Ala; LOW | synonymous_codon | Average:70.922; most accessible tissue: Zhenshan97 root, score: 86.891 | N | N | N | N |