TABLE 2.

Dairy cow phenotypes or characteristics measured from the RDQMA farms and included in our GWAS analyses

Phenotype/characteristic	Positive state (1)	Alternative state (0)	Na
Source	Cow was homebred	Cow was purchased	304
Environment	Isolate was sampled from cow’s environment	Isolate was sampled directly from cow, including fecal and tissue samples	314
LactIndex	Milk yield of cow decreased over lifetime compared to herd mates	Milk yield of cow stayed constant or improved over lifetime compared to herd mates	56
SeroStatus	Cow had at least one positive ELISA	Cow had no positive ELISA	229
ODcat	∼Highest 10% OD values in ELISA of cow serum	∼0–90th percentile of OD values in ELISA of cow serum	229
STpos	Cow was MAP culture positive in tissue (with or without additional positive feces or serum samples)	Cow was only MAP culture positive in feces	160
AnteFC	Cow had at least one MAP-positive fecal culture during lifetime (ante mortem)	Only samples taken from the cow’s carcass after culling/slaughter (post mortem) were MAP culture positive	229
FFS < 3	Cow had first positive MAP fecal sample before the age of 3 yr	Cow had first positive MAP fecal sample at age of 3 yr or older	229
FecalShedGroup	Had at least one sample with >50 CFU/tube (no tissue), high fecal to super shedder	Negative samples or moderate fecal shedder (<50 CFU/tube)	314
Prog	Progressors show an increase in CFU number over time (fecal or tissue)	Nonprogressors show no increase in CFU number (fecal or tissue)	131

^aN refers to the number of measurements made for the corresponding phenotype and for which a MAP isolate was also sequenced.