Episodic Ataxia (EA) pedigree: LOD score
Overall Location Scores from SimWalk2 2.91
MENDEL version 3.35 by Ken Lange is used in the computation of these results
This file contains the location scores calculated using ALL pedigrees.
These location scores are directly comparable to multipoint LOD scores.
All location scores and log-likelihoods are in log10 units.
All the parameters used to set up this run, including the marker map
and penetrance model, if any, are listed at the end of this file.
Alpha is the name given to the 'a priori' proportion of linked pedigrees,
i.e., if there is a trait locus in this region, alpha is the proportion
of these pedigrees that contains an affected genotype at this trait locus.
So, alpha = 1.00 implies no locus heterogeneity.
The value for alpha is set using Batch Item #13.2. When the user sets a value
for alpha < 1.0, then the location scores assumming that value are also shown.
The following tables are comma-delimited to facilitate graphing these results.
The first table below lists the largest location score found in the
analysis of each pedigree individually. (Only the pedigrees within
this run are listed.) Also listed for each pedigree is the first
position that had this score, given in distance (in sex-average Haldane cM)
from the first marker in this study.
, , , LARGEST ,
PEDIGREE, PEDIGREE , POSITION , LOCATION SCORE ,
NUMBER , NAME , in Haldane cM , when alpha=1.00 ,
001 , 20 , 6.6609 , 3.560 ,
The remaining results in this file are calculated by combining
ALL the pedigrees in this study (including any previous runs that
were 'continued' into this run).
The overall log-likelihood considering ONLY THE TRAIT is: -8.554
The overall log-likelihood considering ONLY THE MARKERS is: -333.414
The following table lists the overall location scores for positions
(measured in sex-average Haldane cM) throughout the specified markers.
The overall scores are listed for alpha=1.0 and for any requested,
specific alpha value. The maximum location score allowing for locus
heterogeneity is also reported, maximized over a grid of possible
values for alpha: 0.00, 0.05, 0.10, 0.15, ..., 0.90, 0.95, and 1.0.
Finally, the alpha value (from this grid) that corresponds to this maximum,
heterogeneous location score, is also listed for each position.
MARKER , POSITION , LOCATION SCORE , , MAX HETEROGEN , ALPHA
NAME , Haldane cM , alpha=1.00 , , LOCATION SCORE , VALUE
, -49.9999 , 1.548 , , 1.548 , 1.00
, -45.0000 , 1.700 , , 1.700 , 1.00
, -40.0000 , 1.862 , , 1.862 , 1.00
, -35.0000 , 2.033 , , 2.033 , 1.00
, -30.0000 , 2.212 , , 2.212 , 1.00
, -25.0000 , 2.396 , , 2.396 , 1.00
, -20.0000 , 2.581 , , 2.581 , 1.00
, -15.0000 , 2.760 , , 2.760 , 1.00
, -10.0000 , 2.918 , , 2.918 , 1.00
, -5.0000 , 3.016 , , 3.016 , 1.00
, -0.0001 , 2.870 , , 2.870 , 1.00
S91
, 0.0001 , 2.870 , , 2.870 , 1.00
, 0.1010 , 2.844 , , 2.844 , 1.00
, 0.2020 , 2.817 , , 2.817 , 1.00
, 0.3030 , 2.787 , , 2.787 , 1.00
, 0.4041 , 2.756 , , 2.756 , 1.00
, 0.5051 , 2.722 , , 2.722 , 1.00
, 0.6061 , 2.685 , , 2.685 , 1.00
, 0.7071 , 2.644 , , 2.644 , 1.00
, 0.8081 , 2.599 , , 2.599 , 1.00
, 0.9091 , 2.550 , , 2.550 , 1.00
, 1.0100 , 2.493 , , 2.493 , 1.00
S100
, 1.0102 , 2.493 , , 2.493 , 1.00
, 1.1111 , 2.488 , , 2.488 , 1.00
, 1.2122 , 2.483 , , 2.483 , 1.00
, 1.3132 , 2.478 , , 2.478 , 1.00
, 1.4142 , 2.473 , , 2.473 , 1.00
, 1.5152 , 2.468 , , 2.468 , 1.00
, 1.6162 , 2.463 , , 2.463 , 1.00
, 1.7172 , 2.457 , , 2.457 , 1.00
, 1.8182 , 2.451 , , 2.451 , 1.00
, 1.9193 , 2.445 , , 2.445 , 1.00
, 2.0202 , 2.439 , , 2.439 , 1.00
CACNL1A1
, 2.0204 , 2.439 , , 2.439 , 1.00
, 2.3296 , 2.421 , , 2.421 , 1.00
, 2.6390 , 2.401 , , 2.401 , 1.00
, 2.9484 , 2.380 , , 2.380 , 1.00
, 3.2578 , 2.356 , , 2.356 , 1.00
, 3.5672 , 2.330 , , 2.330 , 1.00
, 3.8765 , 2.301 , , 2.301 , 1.00
, 4.1859 , 2.270 , , 2.270 , 1.00
, 4.4953 , 2.236 , , 2.236 , 1.00
, 4.8047 , 2.199 , , 2.199 , 1.00
, 5.1139 , 2.158 , , 2.158 , 1.00
S372
, 5.1141 , 2.159 , , 2.159 , 1.00
, 5.4234 , 3.149 , , 3.149 , 1.00
, 5.7328 , 3.378 , , 3.378 , 1.00
, 6.0422 , 3.490 , , 3.490 , 1.00
, 6.3515 , 3.544 , , 3.544 , 1.00
, 6.6609 , 3.560 , , 3.560 , 1.00
, 6.9703 , 3.542 , , 3.542 , 1.00
, 7.2797 , 3.484 , , 3.484 , 1.00
, 7.5891 , 3.367 , , 3.367 , 1.00
, 7.8984 , 3.122 , , 3.122 , 1.00
, 8.2077 , 1.506 , , 1.506 , 1.00
pY2/1
, 8.2079 , 1.499 , , 1.499 , 1.00
, 8.3088 , 1.503 , , 1.503 , 1.00
, 8.4098 , 1.506 , , 1.506 , 1.00
, 8.5109 , 1.508 , , 1.508 , 1.00
, 8.6119 , 1.509 , , 1.509 , 1.00
, 8.7129 , 1.510 , , 1.510 , 1.00
, 8.8139 , 1.509 , , 1.509 , 1.00
, 8.9149 , 1.508 , , 1.508 , 1.00
, 9.0159 , 1.506 , , 1.506 , 1.00
, 9.1169 , 1.503 , , 1.503 , 1.00
, 9.2178 , 1.499 , , 1.499 , 1.00
pY21/1
, 9.2180 , 1.499 , , 1.499 , 1.00
, 9.3190 , 1.503 , , 1.503 , 1.00
, 9.4200 , 1.506 , , 1.506 , 1.00
, 9.5210 , 1.508 , , 1.508 , 1.00
, 9.6220 , 1.509 , , 1.509 , 1.00
, 9.7230 , 1.510 , , 1.510 , 1.00
, 9.8240 , 1.509 , , 1.509 , 1.00
, 9.9250 , 1.508 , , 1.508 , 1.00
, 10.0261 , 1.506 , , 1.506 , 1.00
, 10.1271 , 1.503 , , 1.503 , 1.00
, 10.2280 , 1.499 , , 1.499 , 1.00
KCNA5
, 10.2282 , 1.499 , , 1.499 , 1.00
, 10.3291 , 1.503 , , 1.503 , 1.00
, 10.4301 , 1.506 , , 1.506 , 1.00
, 10.5311 , 1.508 , , 1.508 , 1.00
, 10.6321 , 1.509 , , 1.509 , 1.00
, 10.7331 , 1.510 , , 1.510 , 1.00
, 10.8342 , 1.509 , , 1.509 , 1.00
, 10.9352 , 1.508 , , 1.508 , 1.00
, 11.0362 , 1.506 , , 1.506 , 1.00
, 11.1372 , 1.503 , , 1.503 , 1.00
, 11.2381 , 1.499 , , 1.499 , 1.00
S99
, 11.2383 , 1.499 , , 1.499 , 1.00
, 11.3392 , 1.497 , , 1.497 , 1.00
, 11.4402 , 1.493 , , 1.493 , 1.00
, 11.5413 , 1.489 , , 1.489 , 1.00
, 11.6423 , 1.484 , , 1.484 , 1.00
, 11.7433 , 1.478 , , 1.478 , 1.00
, 11.8443 , 1.471 , , 1.471 , 1.00
, 11.9453 , 1.463 , , 1.463 , 1.00
, 12.0463 , 1.454 , , 1.454 , 1.00
, 12.1473 , 1.445 , , 1.445 , 1.00
, 12.2483 , 1.434 , , 1.434 , 1.00
S93
, 12.2485 , 1.435 , , 1.435 , 1.00
, 17.2484 , 2.802 , , 2.802 , 1.00
, 22.2484 , 2.781 , , 2.781 , 1.00
, 27.2484 , 2.654 , , 2.654 , 1.00
, 32.2484 , 2.492 , , 2.492 , 1.00
, 37.2484 , 2.319 , , 2.319 , 1.00
, 42.2484 , 2.145 , , 2.145 , 1.00
, 47.2484 , 1.973 , , 1.973 , 1.00
, 52.2484 , 1.808 , , 1.808 , 1.00
, 57.2484 , 1.652 , , 1.652 , 1.00
, 62.2483 , 1.504 , , 1.504 , 1.00
For alpha = 1.00, the largest overall location score is: 3.560
at position (in Haldane cM): 6.6609
On the alpha grid, the largest overall location score is: 3.560
at position (in Haldane cM): 6.6609
obtained by using an alpha value of: 1.000
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Episodic Ataxia (EA) pedigree: LOD score
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 0.225 0.400 0.83532 1
1.010 S100
0.01000 0.203 0.400 0.85190 2
2.020 CACNL1A1
0.03000 1.014 1.200 0.69886 3
5.114 S372
0.03000 2.727 1.200 0.16172 4
8.208 pY2/1
0.01000 0.320 0.400 0.76368 5
9.218 pY21/1
0.01000 1.078 0.400 0.29520 6
10.228 KCNA5
0.01000 0.087 0.400 0.93812 7
11.238 S99
0.01000 0.373 0.400 0.72406 8
12.248 S93
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Episodic Ataxia (EA) pedigree: LOD score
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: LOCATION SCORE
# 2 Integer label attached to the output files: 22
# 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
#13.2 'A priori' proportion of linked pedigrees: 1.000
#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 Trait penetrances filename: PEN.DAT
Model at the trait locus named: EA
ALLELE FREQUENCY
1 0.99990
2 0.00010
PHENOTYPE COMPATIBLE ORDERED GENOTYPES
1 1/1 1/2 2/2
1 2/1
2 1/1 1/2 2/2
2 2/1
PHENOTYPE/LIABILITY PENETRANCES FOR UNORDERED GENOTYPES:
CLASS 1/1 1/2 2/2
101 0.999000 0.010000 0.010000
201 0.001000 0.990000 0.990000
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 1000
#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: 0
#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: 5200000
All relevant 'Run-Specifying Parameters' are at their default values.
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