Search for Variation information by Variation ID:

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

Detailed information for vg0141376024:

Variant ID: vg0141376024 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41376024
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCTCTTCCAGCCGACCACGGCGACGGTGGCCGACGACGGACGGACATACAGCAACATGTTCGCCGCGATGGTGGACGCCATGTACTCGGCGTTGGAGAA[G/A]
GCCGGGGCGCCGGGGGTGGCCGTCGTCGTGTCCGAGAGCGGGTGGCCGTCGGCCGGCGGCTCCGGCGCGAGCGCGGACAACGCGCGGAGGTACAACCAGG

Reverse complement sequence

CCTGGTTGTACCTCCGCGCGTTGTCCGCGCTCGCGCCGGAGCCGCCGGCCGACGGCCACCCGCTCTCGGACACGACGACGGCCACCCCCGGCGCCCCGGC[C/T]
TTCTCCAACGCCGAGTACATGGCGTCCACCATCGCGGCGAACATGTTGCTGTATGTCCGTCCGTCGTCGGCCACCGTCGCCGTGGTCGGCTGGAAGAGGG

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 96.20% 3.70% 0.04% 0.00% NA
All Indica  2759 99.50% 0.50% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 39.80% 59.90% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.70% 0.13% 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 99.00% 1.00% 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
vg0141376024 G -> A LOC_Os01g71410.1 synonymous_variant ; p.Lys273Lys; LOW synonymous_codon Average:71.678; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N