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Detailed information for vg0905621124:

Variant ID: vg0905621124 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5621124
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTTGCAAATCTTGCGACGGTTCCAATTTTCCCTCTCATGAGCTGCTTTCCGCCGCTCCAC[G/A]
CCAACTGCATCCATGGCGCAAAGCATATACACGCCATGCTTCAGAGTGGTGCTATCTTCATCTTCCGGGCAATTGTAAACTCCATACTCCTGATCATGAA

Reverse complement sequence

TTCATGATCAGGAGTATGGAGTTTACAATTGCCCGGAAGATGAAGATAGCACCACTCTGAAGCATGGCGTGTATATGCTTTGCGCCATGGATGCAGTTGG[C/T]
GTGGAGCGGCGGAAAGCAGCTCATGAGAGGGAAAATTGGAACCGTCGCAAGATTTGCAAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCCG

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 99.10% 0.90% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 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 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 66.70% 33.30% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0905621124 G -> A LOC_Os09g10310.1 synonymous_variant ; p.Gly135Gly; LOW synonymous_codon Average:54.016; most accessible tissue: Zhenshan97 young leaf, score: 69.723 N N N N