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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.