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Output
Here is a truncated example of the output of Zmapqtl for a backcross.
# 890840384 filetype Zmapqtl.out
#
# QTL Cartographer V. 1.13b, March 1998
# This output file (qtlcart.z) was created by Zmapqtl...
#
# It is 10:39:44 on Wednesday, 25 March 1998
#
#
#The position is from the left telomere on the chromosome
window 10.00 Window size for models 5 and 6
background 5 Background parameters in model 6
Model 6 Model number
trait 1 Analyzed trait [Trait_1]
cross B2 Cross
# Test Site * Like. Ratio Test Statistics * Additive
c m position H0:H1 R2(0:1) TR2(0:1) H1:a S1
s
1 1 0.0001 0.411 0.002 0.473 0.027 1.531
1 2 0.0133 0.016 0.000 0.472 0.005 1.542
1 2 0.0333 0.023 0.000 0.472 0.006 1.547
1 2 0.0533 0.031 0.000 0.472 0.008 1.554
1 2 0.0733 0.041 0.000 0.472 0.009 1.563
1 2 0.0933 0.052 0.000 0.472 0.010 1.572
1 2 0.1133 0.063 0.000 0.472 0.011 1.582
1 2 0.1333 0.073 0.000 0.472 0.012 1.593
.
.
.
e
For a backcross, let be the additive effect. We have two hypotheses:
 : no QTL effect at the test position, i.e.
 : There is a QTL effect at the test position, i.e.
The first eight columns correspond to
 Chromosome of test position
 Left flanking marker of test position
 Absolute position from left telomere, in Morgans.
 Likelihood ratio test statistic for
It is a
random variable with one degree of freedom for any position, meaning that a
value of 3.84 or higher is evidence for a QTL. The significance level over more
positions will be higher due to multiple testing.


 Estimate of (the additive effect) under
 Test statistic for the normality of the residuals under
The last 13 columns are not shown because they are only valid for design experiments.
They would all be zeros if shown.
The output for an design (or any design in which dominance effects can be estimated)
is similar, but has more information.
For an , you can estimate additive () and dominance () parameters at each
position. Thus, there are four hypotheses.
and twelve full columns of output, corresponding to all possible hypothesis tests
and parameter estimates.
The 21 columns correspond to
 Chromosome of test position.
 Left flanking marker of test position.
 Absolute position from left telomere, in Morgans.
 Likelihood ratio test statistic for
 Likelihood ratio test statistic for
 Likelihood ratio test statistic for
 Estimate of (the additive effect) under
 Estimate of (the additive effect) under
 Estimate of (the dominance effect) under
 Estimate of (the dominance effect) under
 Likelihood ratio test statistic for
 Likelihood ratio test statistic for
 for
 for
 for
 for
 for
 for
 for
 for
 for
Subsections
Next: Permutation Test output
Up: Zmapqtl
Previous: Permutations, Bootstraps and Jackknives
Contents
Index
Christopher Basten
20020327