Default error rate for Illumina

[mbhall88]

I'm wondering where the default error rate (for Illumina) of 0.05 (5%) comes from? That is awfully high for Illumina - most sources I read (and pandora) use something more like 0.001 (0.1%).

mykrobe/src/mykrobe/base.py

Lines 124 to 130 in 59dfb97

	genotyping_mixin.add_argument(
	"-e",
	"--expected_error_rate",
	help="Expected sequencing error rate (default: %(default).2f)",
	default=0.05,
	type=float,
	)

While working on mbhall88/head_to_head_pipeline#76 I tried out lowering the error rate to 0.001. It didn't have a huge impact, but all the differences were positive. We recovered one FN for Ethambutol and one FN for Rifampicin.

@martinghunt I wonder if you played with the error rate when doing the analysis for the recent paper? If not, how easy would it be to rerun it with this lowered error rate to see the impact on a bigger dataset?