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Detailed information for vg0226609469:

Variant ID: vg0226609469 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26609469
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary 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. )

Flanking Sequence (100 bp) in Reference Genome:


CAAACCAAGCCGTCGGTAGGTCAGAAATGAAACATACTACTGTACATATCAAACCGGAAAATGCGTTGAGCTCACCATAGGCAATGGCGGATCCGACGCC[A/G]
GCGAAGACGAAGAGGAGGGTGGCGATGAACTCCGCCACGTAGGCCTTCACGGACGTGGCGCTGAAGGAGTCACCCAAGCTTCCGAATGCGAGCTTCACCA

Reverse complement sequence

TGGTGAAGCTCGCATTCGGAAGCTTGGGTGACTCCTTCAGCGCCACGTCCGTGAAGGCCTACGTGGCGGAGTTCATCGCCACCCTCCTCTTCGTCTTCGC[T/C]
GGCGTCGGATCCGCCATTGCCTATGGTGAGCTCAACGCATTTTCCGGTTTGATATGTACAGTAGTATGTTTCATTTCTGACCTACCGACGGCTTGGTTTG

Allele Frequencies:

Populations Population SizeFrequency 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

Allele Effect:

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