Table 1 Performance of HLA target-enrichment experiments.

From: Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations

 

Sequence data

Min

Max

Median (95% CI)

endogenous [%]

original

1

76

14 (8–25)

HLA-enriched

2

88

36 (24–42)

reads aligning to HLA genes [%]

original

0.00

0.02

0.00 (0.00–0.00)

HLA-enriched

0.00

0.39

0.12 (0.05–0.17)

average HLA coverage [%]

original

0

93

7 (5–13)

HLA-enriched

2

100

97 (94–99)

average HLA read depth (x-fold)

original

0.00

3.98

0.14 (0.11–0.22)

HLA-enriched

0.12

472.62

18.00 (9.68–68.95)

  1. Endogenous DNA content (%), percentage of reads aligning to HLA genes (%), average HLA coverage (%) and average HLA read depth (x-fold) compared between pre-capture shotgun sequence data (original) and sequence data after HLA enrichment experiments (HLA-enriched) obtained from a subset of 62 historical samples.
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