Table 1. Summary of ALL data analysis.

Analysis information	Count	Overall	%
Default vs. Manual	4013	4473	89.7
Reproducibility 1 - Default	1004	1330	75.5
Reproducibility 1 - Manual	1251	1330	94.1
Reproducibility 2 - Default	986	1137	86.7
Reproducibility 2 - Manual	1234	1236	99.8
NA calls - Default	142	4473	3.2
NA calls - Manual	118	4473	2.6
THR calls - Default	220	4473	4.9
THR calls - Manual	37	4473	0.8
Accuracy 1 - Default	3860	4473	86.3
Accuracy 1 - Manual	4299	4473	96.1
Accuracy 2 - Default	3860	4111	93.9
Accuracy 2 - Manual	4299	4318	99.6

Results represent a pooled analysis of the 3 SNPs comparing calls made using either the default or manual settings of the software. The genotypes that can not be called are sub-divided in two classes: NA calls which correspond to an inappropriate normalized fluorescent value outside of confidence intervals and THR calls, which correspond to raw fluorescence under the minimal threshold. Accuracy, which represents the percent of ALG calls similar to the calls obtained by sequencing experiments, and reproducibility are measured in each condition. Reproducibility and accuracy are measured when all calls are taken into account (1) or when only genotypic calls are considered (2, no Na and THR calls). Measures are reported in terms of number of SNPs specifically called, the overall number of SNPs called and the corresponding percentage.