(Index)    sample    reads yeasts
9          CO ref    10
10         CO raai   20
11         CO tus    30

(Index)    sample    reads yeasts
9          CO ref    10
11         CO tus    30
10         CO raai   10

df=fd.reindex(["CO ref","CO tus","CO raai"])

df.index=["CO ref","CO tus","CO raai"]

df["sample"].index=["CO ref","CO tus","CO raai"]

df=fd.set_index('sample').reindex(["CO ref","CO tus","CO raai"]).reset_index()