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Table 2 Statistics of HLA typing results from 51 HapMap samples

From: HLAreporter: a tool for HLA typing from next generation sequencing data

Quality standard (QS) a

HLA gene

Total number of genes

Number of QS passes a

Pass QS (%) a

Four-digit (%) b

Two-digit (%) b

10 × = 100% and 20× ≥98%

HLA-A

51

3

6%

100%

100%

 

HLA-B

51

7

14%

100%

100%

 

HLA-C

51

4

8%

100%

100%

 

HLA-DRB1

46

28

61%

100%

100%

 

HLA-DQB1

51

20

39%

100%

100%

 

HLA-DQA1

51

20

39%

100%

100%

10 × = 100% and 20× ≥90%

HLA-A

51

18

35%

81%

100%

 

HLA-B

51

18

35%

83%

100%

 

HLA-C

51

11

22%

100%

100%

 

HLA-DRB1

46

40

87%

99%

100%

 

HLA-DQB1

51

27

53%

100%

100%

 

HLA-DQA1

51

35

69%

100%

100%

10× ≥95%

HLA-DRB1

46

45

98%

96%

98%

 

HLA-DQB1

51

46

90%

91%

99%

 

HLA-DQA1

51

43

84%

100%

100%

  1. aQuality standard (QS) ‘10 × ’ represents the percentage of locations with coverage depth greater than 10-fold on the targeted exon. Accordingly, ‘10× ≥95%’ means the pre-defined percentage (that is, ‘10 × ’) is 95% or above. (‘20 × ’ has a similar definition). bThe four-digit (two-digit) percentage is equal to the number of HLA calls at four-digit (two-digit) resolution without ambiguity divided by the total number of alleles.
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Genome Medicine

ISSN: 1756-994X

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