command

awk '$6 >= 0.01' file.txt

output

chr     pos         ref var p.val       freq.var
chr19   9074573     A   C   6.73E-22    0.586593469
chr19   9091288     G   T   5.96E-188   0.508732726
chr12   56490398    G   T   0.005271732 0.010003218
chr12   56477619    G   A   1.40E-15    0.010001069
chr12   56477619    G   A   1.40E-15    0.010001069
chr3    52677261    C   T   5.13E-06    0.01
chr5    67591010    A   G   4.82E-23    0.01

command

awk '$6 >= 0.01' file.txt

output

chr     pos         ref var p.val       freq.var
chr19   9074573     A   C   6.73E-22    0.586593469
chr19   9091288     G   T   5.96E-188   0.508732726
chr12   56490398    G   T   0.005271732 0.010003218
chr12   56477619    G   A   1.40E-15    0.010001069
chr12   56477619    G   A   1.40E-15    0.010001069
chr3    52677261    C   T   5.13E-06    0.01
chr5    67591010    A   G   4.82E-23    0.01

Python

#!/usr/bin/python

k=open('file.txt','r')
k.readline()
print ("chr     pos         ref var p.val       freq.var")
for i in k:
    q=i.split(' ')[-1]
    if (float(q) >= 0.01):
        print (i.strip())



output

chr     pos         ref var p.val       freq.var
chr19   9074573     A   C   6.73E-22    0.586593469
chr19   9091288     G   T   5.96E-188   0.508732726
chr12   56490398    G   T   0.005271732 0.010003218
chr12   56477619    G   A   1.40E-15    0.010001069
chr12   56477619    G   A   1.40E-15    0.010001069
chr3    52677261    C   T   5.13E-06    0.01
chr5    67591010    A   G   4.82E-23    0.01