Table 16 Root mean squared error (RMSE) between the gold standard and estimated STR sizes with allelotype using the original BAM file for NA12878 from HiSeq 2000 and those realigned with STR-realigner, ReviSTER, GATK IndelRealigner, and allelotype with --realign option for all the STR regions

1

5345

2.298

2.294

2.354

2.296

2.298

2

1160

3.152

3.293

3.265

3.243

3.129

3

517

2.033

2.039

2.034

2.038

2.034

4

1433

2.453

2.582

2.687

2.600

2.454

5

668

3.033

3.006

3.271

3.008

3.031

6

472

2.698

2.739

2.765

2.739

3.090

Total

9595

2.503

2.542

2.607

2.538

2.521