AAT Bioquest

What are the differences between exome sequencing and whole genome sequencing?

Posted December 5, 2022




Exome sequencing (WES) and whole genome sequencing (WGS) are two next generation sequencing (NGS) techniques that are widely used in healthcare to study genetic anomalies. There are several differences between these two processes.

Basis of differentiationExome sequencing (WES)Whole genome sequencing (WGS)
Definition Is the process of sequencing coding DNA (exomes) of an organism Is the process of sequencing the whole genome of an organism including all coding and noncoding regions
Percentage of genome sequencedSequences coding genomes which maek up only 1-2% of hte whole genomeSequences all coding, noncoding, and mitochondrial genomes, which make up 98 – 99% of the whole genome
Area of studyUsed to determine genetic variations in coding regionsUsed to study genetic rearrangements and anomalies in coding and noncoding regeions
Size of sequence database generatedSequence database generated is comparatively smaller than WGSSequence database generated is very large and sometimes incomprehensible
Time takenIs less time-comsuming than WGSIs a time-consuming process
CostCheaperMore expensive
  • Generates smaller, more manageable data sets that make data analysis faster and  cheaper;
  • Provides comprehensive coverage of coding sequences;
  • Identifies variants across a wide range of applications:
  • Is a faster and more cost-effective alternative to WGS
  • Delivers large volumes of data in a short amount of time to support asembly of novel genomes;
  • Provides a high-level comprehensive view of the entire genome;
  • Captures both large and small variants that are often missed with targeted approaches such as WES;
  • Can be used to sequence coding as well as noncoding regions, which are sometimes responsible for genetic disorders
DisadvantagesUnable to identify anomalies in noncoding sequences
  • Is an expensive and time-consuming process; 
  • create very large data sets that are sometimes incomprehensible


Additional resources

Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions


Sanger Sequencing