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Properly paired reads

Definition
AI-generated

Properly paired reads are a mate pair whose orientations and separation fall within expected insert-size limits for the library, as encoded in SAM flags after alignment.

Topics
Sequencing Data Analysis
Related
Insert size Paired-End Sequencing

Why it matters in GWAS

Discordant pairs motivate SV discovery; loss of proper pairing can signal contamination, degradation, or library failure.

Example usage

"The fraction of properly paired reads fell below 90% in two samples that were excluded."

Insert size Paired-End Sequencing
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Li H, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics.
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