Table 15 Root mean squared error (RMSE) between the gold standard and estimated STR sizes with RepeatSeq using the original BAM file for NA12878 from HiSeq 2000 and those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner for all the STR regions

1

5345

2.429

2.397

2.431

2.430

2

1160

3.587

3.860

3.829

3.804

3

517

1.901

1.902

2.000

1.998

4

1433

2.509

2.540

2.709

2.710

5

668

3.134

2.736

3.021

3.039

6

472

2.821

2.823

2.890

2.890

Total

9595

2.656

2.660

2.724

2.721