Why the sweed output has the majority of the likelihoods as 0

[vineeth m r]

Hello,

I am using sweed to find the likelihoods, but  in the results majority of the likelihoods are 0.  Is this normal?

SweeD version 3.2.11

Genome size is 84648390

Command: ./SweeD-P -threads 4 -name bta14folded -folded -input /media/work/A0C6F5AEC6F584B6/work/snpbt/Bindallsnponly.ann.canononlyprot.rs.d10Q30D500.14.recode.vcf -grid 1000000

Regards

Vineeth M R

/1
Position    Likelihood    Alpha
36545.0000    4.722475e-01    3.902012e+01
36626.3292    0.000000e+00    4.000000e-01
36707.6584    0.000000e+00    1.081081e-01
36788.9876    0.000000e+00    6.250002e-02
36870.3168    0.000000e+00    4.379563e-02
36951.6460    0.000000e+00    3.380283e-02
37032.9752    0.000000e+00    2.752295e-02
37114.3044    0.000000e+00    2.316602e-02
37195.6336    0.000000e+00    2.003339e-02
37276.9628    0.000000e+00    1.764706e-02
37358.2920    0.000000e+00    1.574803e-02
37439.6212    0.000000e+00    1.423488e-02
37520.9504    0.000000e+00    1.298702e-02
37602.2796    0.000000e+00    1.192843e-02
37683.6088    0.000000e+00    1.103956e-02
37764.9380    0.000000e+00    1.027398e-02
37846.2672    0.000000e+00    9.600003e-03
37927.5964    0.000000e+00    9.015780e-03
38008.9256    0.000000e+00    8.498585e-03
38090.2548    0.000000e+00    8.032131e-03
38171.5840    0.000000e+00    7.619048e-03
38252.9132    0.000000e+00    7.246377e-03
38334.2424    0.000000e+00    6.904489e-03
38415.5716    0.000000e+00    6.597033e-03
38496.9008    0.000000e+00    6.315790e-03
38578.2300    0.000000e+00    6.054492e-03
38659.5592    0.000000e+00    5.816772e-03
38740.8884    0.000000e+00    5.597017e-03
38822.2176    0.000000e+00    5.390837e-03
38903.5468    0.000000e+00    5.201561e-03
38984.8760    0.000000e+00    5.025126e-03
39066.2052    0.000000e+00    4.858301e-03
39147.5344    0.000000e+00    4.704038e-03
39228.8636    0.000000e+00    4.559271e-03
39310.1928    0.000000e+00    4.421519e-03
39391.5220    0.000000e+00    4.293382e-03
39472.8512    0.000000e+00    4.172463e-03
39554.1804    0.000000e+00    4.056796e-03

[Pavlos Pavlidis]

This is because the likelihood of the neutral model is higher or equal to the value of the sweep model. 

All the best 

Pavlos 

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[vineeth m r]

Thank you

Dr. Vineeth M.R
Ph.D Scholar
Molecular Genetics Lab
ICAR-NDRI
Karnal, Haryana
132001