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Table 3 Number of false-negatives when different steps in the pipeline omitted

From: Edge effects in calling variants from targeted amplicon sequencing

u(minimum distance of the Uracil base from 3’ end of primer) No. of simulated variants False-negatives
   Without BAQ and BQSR With BQSR and without BAQ With BAQ and without BQSR Default pipeline (with both BAQ and BQSR)
1 15,871 8 669 3,725 2,830
2 15,871 9 23 775 397
3 15,871 3 3 136 37
4 15,871 1 1 59 13
5 15,871 0 0 35 5
6 15,871 0 0 20 2
7 15,871 0 0 23 1
8 15,871 0 0 28 0