New who mutations

[jodyphelan]

Add in high-confidence mutations released in the WHO catalogue (https://www.who.int/publications/i/item/9789240028173).

Performance notes

Using a dataset of 32672 isolates for which we have WGS data and DST we looked at the performance when adding in new mutations. Below is the sensitivity and specificity for the old mutation list and the new (old + who mutations).

In a nutshell - sensitivity increases for most drugs and specificity drops a bit in some.

Drug	Old Sens	Old Spec	New Sens	New Spec
streptomycin	0.82	0.94	0.84	0.93
ethambutol	0.91	0.91	0.91	0.91
isoniazid	0.93	0.98	0.93	0.98
para-aminosalicylic_acid	0.39	0.95	0.39	0.95
cycloserine	0.3	0.96	0.3	0.96
amikacin	0.77	0.99	0.79	0.98
kanamycin	0.88	0.98	0.88	0.98
pyrazinamide	0.86	0.96	0.89	0.96
ofloxacin	0.85	0.97	0.85	0.97
ciprofloxacin	0.92	0.99	0.92	0.99
capreomycin	0.76	0.97	0.76	0.97
rifampicin	0.95	0.98	0.96	0.98
ethionamide	0.7	0.79	0.82	0.7
levofloxacin	0.97	0.95	0.97	0.95
moxifloxacin	0.83	0.88	0.83	0.88