Table 3

HLA calling accuracy and concordance with gold standard in 270 individuals

Population

Concordant alleles

Original type missing

Original type incorrect

Incorrect call due to low coverage

Incorrect due to other reasons

Total

Accuracy


CEU

457

66

6

10

1

540

(= 90 × 6)

97.7%

(463/474)


YRI

485

8

16

29

2

540

(= 90 × 6)

94.2%

(501/532)


JPT

246

6

9

5

4

270

(= 45 × 6)

96.6%

(255/264)


CHB

258

0

7

5

0

270

(= 45 × 6)

98.1%

(265/270)


Total

1446

80

38

49

7

1620

96.4%


Erlich et al. BMC Genomics 2011 12:42   doi:10.1186/1471-2164-12-42

Open Data