Episodic Ataxia (EA) pedigree: Sampling 
     
                      Recombination Statistics from SimWalk2 2.91
     
     
 Here, for each marker interval, is the number of recombinations observed
 and the number expected, given the total number of meioses & the interval size.
     
 The 'observed value' listed below is the average over all pedigrees that were
 sampled during the MCMC phase. Thus, this value is an estimate of the average
 over all possible configurations each weighted by its likelihood, i.e.,
 given the data, this is our best estimate of the true value.
     
 We also estimate the p-value for these observations, i.e., the probability that
 one would observe this many recombination events OR MORE within this interval,
 again given the total number of meioses & the interval size. A very small
 p-value indicates that the number of observed recombinations would be more
 consistent with a larger recombination distance for this marker interval.
 Similarly, a p-value close to 1 indicates that the user-specified recombination
 distance for this interval should be re-evaluated and perhaps made smaller.
 Such extreme p-values are flagged when they appear.
     
     
 The total number of pedigrees actually analyzed here:              1
 The total number of meioses contained in these pedigrees:         40
     
 Since the user-specified recombination distances are sex-independent,
 we report the combined female and male recombination statistics.
     
     
     
                     OVERALL RECOMBINATION STATISTICS
     
     
 POSITION   MARKER     RECOMB.   RECOMBINATION EVENTS   SIGNIFICANCE    INTERVAL
Haldane cM   NAME     FRACTION    OBSERVED & EXPECTED     (P-VALUE)      NUMBER 
     
    0.000   S91     
                       0.01000       0.200      0.400      0.85416          1
    1.010   S100    
                       0.01000       0.200      0.400      0.85416          2
    2.020   CACNL1A1
                       0.03000       1.200      1.200      0.62609          3
    5.114   S372    
                       0.03000       2.500      1.200      0.20713          4
    8.208   pY2/1   
                       0.01000       0.300      0.400      0.77872          5
    9.218   pY21/1  
                       0.01000       1.000      0.400      0.33103          6
   10.228   KCNA5   
                       0.01000       0.100      0.400      0.92862          7
   11.238   S99     
                       0.01000       0.400      0.400      0.70406          8
   12.248   S93     
     
     
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                      Episodic Ataxia (EA) pedigree: Sampling 
     
                      Batch Instruction Parameters
     
     
 Below are listed the SimWalk2 2.91 instruction parameters used in this run.
 Also, where appropriate, the default values of the batch items are listed.
     
 (Please see the documentation for a more complete description
  of the meaning of these parameters.)
     
     
Batch                                                                 Actual    
Item              GENERAL PARAMETERS                                  Value     
     
# 1    Type of analysis:                                         PED. SAMPLING 
# 2    Integer label attached to the output files:                      01     
# 3    Title for this run is the above title:                      (see above) 
# 4    Continuation of previous run?                                    NO     
       Number of pedigrees analyzed in this entire run:                  1     
     
     
Batch                                                                 Actual    
Item              INPUT-FILE PARAMETERS                               Value     
     
#09    Map data filename:                                              MAP.DAT 
#10    Locus data filename:                                          LOCUS.DAT 
#11    Pedigree data filename:                                    PEDIGREE.DAT 
#12.1  Symbol for females (case insensitive):                            F     
#12.2  Symbol for   males (case insensitive):                            M     
#13.1  Trait locus included in analyzed data?                          YES     
#16    Affection status is indicated by the label:                       2     
#17    Affection status is indicated at the:                       TRAIT LOCUS 
#18    Number of quantitative variables:                                 1     
#19    No trait penetrances file:                                              
     
Marker Map:
     
POSITION (Haldane cM)    MARKER        RECOMBINATION RATES     INTERVAL 
   FEMALE  &   MALE       ORDER         FEMALE  &   MALE        NUMBER  
    0.000      0.000    S91     
                                       0.01000    0.01000          1
    1.010      1.010    S100    
                                       0.01000    0.01000          2
    2.020      2.020    CACNL1A1
                                       0.03000    0.03000          3
    5.114      5.114    S372    
                                       0.03000    0.03000          4
    8.208      8.208    pY2/1   
                                       0.01000    0.01000          5
    9.218      9.218    pY21/1  
                                       0.01000    0.01000          6
   10.228     10.228    KCNA5   
                                       0.01000    0.01000          7
   11.238     11.238    S99     
                                       0.01000    0.01000          8
   12.248     12.248    S93     
     
     
Batch                                                      Default    Actual    
Item              RUN-SPECIFYING PARAMETERS                 Value     Value     
     
#20    Number of pedigrees sampled for each input pedigree  1000        10    **
#21    Number of parallel runs during simulated annealing:     1         1      
#22    Initial temperature value:                            100.00    100.00   
#23    Temperature change factor:                              0.99      0.99   
#24    Number of temperature changes:                        800       800      
#25    Number of pre-simulated annealing steps:                0         0      
#26    Maximum number of attempts to initialize pedigrees:    64        64      
     
       Number of steps per temperature is roughly:                    5200     
#29.1    using a minimum number of steps of:                1000      1000      
#30.1    and a multiplicative factor of:                      10        10      
       Number of steps per sampled pedigree is roughly:               5200     
#29.2    using a minimum number of steps of:                1000      1000      
#30.2    and a multiplicative factor of:                      10        10      
       Mean number of transitions per step
#31.1    during simulated annealing:                           2.00      2.00   
#31.2    during Markov chain Monte Carlo process:              2.00      2.00   
       Weight factor for individuals untyped at a locus
#32.1    during simulated annealing:                          10        10      
#32.2    during Markov chain Monte Carlo process:             10        10      
       Frequency that next pivot is forced to be nearby
#33.1    during simulated annealing:                           0.50      0.50   
#33.2    during Markov chain Monte Carlo process:              0.50      0.50   
       Frequency that a founder transition is of type 2
#34.1    during simulated annealing:                           0.25      0.25   
#34.2    during Markov chain Monte Carlo process:              0.25      0.25   
#35    Number of steps between free runs:                      0         0      
#36.1  Random seed number 1:                               27713     27713     
#36.2  Random seed number 2:                                2321      2321     
#36.3  Random seed number 3:                               18777     18777     
#37.1  Error model for mistyping:                          uniform   uniform    
#37.2  Overall rate of mistyping:                              0.025     0.025  
     
     
Batch                                                                 Actual    
Item              OUTPUT-FILE PARAMETERS                              Value     
     
#39    Files to output from IBD analysis:                        IBD & KINSHIP 
#40    Output the pedigrees individually in INPED-nn.mmm?               NO     
#41    Output the location scores per pedigree in SCORE-nn.mmm?         NO     
#42    Threshold for mistyping probability to be significant:            0.50  
#43    Export haplotypes for drawing applications?                      NO     
#44.1  Threshold haplotype   count for RERUN-nn.PED entry:               0     
#44.2  Threshold recombinant count for RERUN-nn.PED entry:               0     
#45    Threshold fraction of steps for RERUN-nn.PED entry:               0.85  
#46.1  Output haplotypes in vertical representations?                   NO     
#46.2  Output haplotypes using founder-haplotype labels?                NO     
#46.3  Force allele choice when no allele information exists?           NO     
#47    Output the sampled peds in LINKAGE-format in MODEL-nn.*?         NO     
#48    Num. of unconditional simulations for empirical p-value:      10000     
#49.1  Number of points analyzed within each marker interval:            3     
#49.2  Size of uniform grid interval for analysis positions:             1.00  
     
     
     With the above parameters, the number of steps
       per simulated annealing run is roughly:                     4160000     
       per Markov chain Monte Carlo run is roughly:                  52000     
     
     
** indicates a relevant 'Run-Specifying Parameter'
   that has been altered from its default value.
     
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