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How to interpret output of ContEst
I've recently started using ContEst and now I'd like to understand exactly what I get in the output file. What does each column mean?
-Are "contamination", "confidence_interval_95_width", "confidence_interval_95_low", "confidence_interval_95_high" fractions or percentages?
-What does "sites" represent?
I also have some questions regarding the following statistics printed to the screen:
INFO 14:38:48,617 ContEst - Population informed sites: 314
INFO 14:38:48,618 ContEst - Non homozygous variant sites: 277
INFO 14:38:48,618 ContEst - Homozygous variant sites: 37
INFO 14:38:48,619 ContEst - Passed coverage: 35
INFO 14:38:48,619 ContEst - Results: 10
-What is the coverage threshold which 35 sites have passed here? Can this threshold be set?
-What does the "Results" number refer to? I've noted that it is the same number as in the "sites" column in the output file.