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Detailed information for vg0226608644:

Variant ID: vg0226608644 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26608644
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACACGACGAATATCAAATCAAGCAAACGTACGATGCATGCAAACTGACACGGATACTTCAATTAATTCGGTTCATCCACTTTTAAGCGTAGTCCTGGTC[G/A]
GCAACGGGCTGGTATGAGCCGATGAACACGTCGCCGTACACGAGCCCGGCGAGGCCGCCGCCGATCAGCGGGCCGACCCAGTAGACCCAGTTGCCAGCGA

Reverse complement sequence

TCGCTGGCAACTGGGTCTACTGGGTCGGCCCGCTGATCGGCGGCGGCCTCGCCGGGCTCGTGTACGGCGACGTGTTCATCGGCTCATACCAGCCCGTTGC[C/T]
GACCAGGACTACGCTTAAAAGTGGATGAACCGAATTAATTGAAGTATCCGTGTCAGTTTGCATGCATCGTACGTTTGCTTGATTTGATATTCGTCGTGTG

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 99.90% 0.10% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.40% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0226608644 G -> A LOC_Os02g44080.1 synonymous_variant ; p.Ala243Ala; LOW N Average:72.979; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N