Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1200522149:

Variant ID: vg1200522149 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 522149
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAAGAGCGCGCAGTAGCCGTACTGCGCGAAGCACGTGGCGTGGAGCAGGAGCACGACGACGGCCACGTGGAGGCGCTCGCGGCGCAGGCCGGCGGCGCC[G/A]
TTCTTGCAGTAGAGGGCACGGAGCTCGGCGACGTCGGCGGCGCGCCATCGGAGGAGGAGCGCGAGGTGGTGGCAGAGCTTGGGATGCTGGTAGACGCACA

Reverse complement sequence

TGTGCGTCTACCAGCATCCCAAGCTCTGCCACCACCTCGCGCTCCTCCTCCGATGGCGCGCCGCCGACGTCGCCGAGCTCCGTGCCCTCTACTGCAAGAA[C/T]
GGCGCCGCCGGCCTGCGCCGCGAGCGCCTCCACGTGGCCGTCGTCGTGCTCCTGCTCCACGCCACGTGCTTCGCGCAGTACGGCTACTGCGCGCTCTTCT

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 99.30% 0.70% 0.04% 0.00% NA
All Indica  2759 98.80% 1.10% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.00% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  96 100.00% 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
vg1200522149 G -> A LOC_Os12g01890.1 synonymous_variant ; p.Asn178Asn; LOW synonymous_codon Average:70.594; most accessible tissue: Zhenshan97 flower, score: 85.482 N N N N