Genotyping of selected germline adaptive immune system loci using short-read sequencing data

Table 4.

Mean PPV and proportion of calls passing optimal prefix consistency thresholds by gene type

PPV Passing proportion
Gene type Mean Median Mean Median
IGHV 0.8771 0.9310 0.3390 0.3359
IGLV 0.9633 1.0000 0.9621 0.9756
IGKV 0.8203 0.8966 0.6982 0.7692
TRAV 0.8263 1.0000 0.8786 0.9615
TRGV 0.9342 0.9762 0.9880 1.0000

  • Optimal thresholds selected via F-beta (β = 0.5), prioritizing precision. A lower passing proportion in IGHV reflects locus complexity.

This Article

  1. Published in Advance August 5, 2025, doi: 10.1101/gr.280314.124 Genome Res. 35: 2076-2086

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