Table 3. Genotype reproducibility rates(%)*.

Variant type	Sample ID	Unfiltered	Filtered
HaplotypeCaller/3.4 Bi-allelic SNP Multi-allelic SNP	H119 H137 H151 H119 H137 H151	98.9 97.7 97.8 95.0 92.3 92.1	99.5 98.5 98.3 96.6 94.0 93.6
Bi-allelic indel Multi-allelic indel	H119 H137 H151 H119 H137 H151	98.1 96.3 96.0 91.9 88.0 87.9	98.6 96.8 96.4 93.2 89.3 89.1
Genomestrip/2.0 Deletion	H119 H137 H151	99.7 100.0 100.0	95.6 100.0 100.0
Duplication	H119 H137 H151	99.7 99.9 99.6	100.0 100.0 100.0

*Presented values are the overall genotype concordance, as generated using GATK/3.4 Genotype Concordance function. Code, logs and output data are available at http://doi.org/10.5281/zenodo.160539.