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gchen98 / macs

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Interpreting output #16

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
./macs 100 1e6 -t .001 -r .001 -h 1e2

What is the expected output? What do you see instead?

COMMAND:    ./macs 100 1e6 -t .001 -r .001 -h 1e2
SEED:   1370614464
SITE:   0    0.000184624691    
0.0518626894    0100000000000000010000000000000000110000000100000000100000000000000
000000000100000000000000000000000
SITE:   1    0.000278265467   
0.00288222514   000000000000000000000000000010000000000000000000000000100000000000
0000000000000000000000000000000000
SITE:   2    0.000407719185     
0.449356828 00011000100010001001010100000011000010010000010100010101001011000111
00000011000010001010000101110101
SITE:   3    0.000517977674     
0.443446518 00011000100010001001010100000011000010010000010100010101001011000111
00000011000010001010000101110101
SITE:   4    0.000520646282     
0.021129332 00000000000000000000000000000010000000000000000000000000001010000000
00000000000000000000000000000000
SITE:   5     0.00074230439    
0.0214293894    0000000000000000000000000000000000000000100000000000000000000000000
000000000000000010000000000000000
 and so on

Please provide any additional information below.

Hi Gary,
I am having trouble understanding the third column of the output. I understand 
the first column is the site number and the second is the position (in what 
units?). The last column, each 0 or 1 represents an individual with or without 
the variant. But what is the third column?
In particular, my goal is to find the time a mutation occurs (in generations or 
coalescent units). I don't think ms has this function so I was hoping your 
version might.
Thanks!

Original issue reported on code.google.com by Rothwell...@gmail.com on 7 Jun 2013 at 3:32

GoogleCodeExporter commented 9 years ago 
It's your lucky day. The third column is mutation time in 4n generations.

Original comment by gche...@gmail.com on 7 Jun 2013 at 4:24