Episodic Ataxia (EA) pedigree: Haplotype
Haplotyping Results from SimWalk2 2.91
The results for the pedigree named: 20
which is pedigree number: 001
This haplotype run has the label: 11
The number of individuals is: 29
NAME MOTHER FATHER SEX TRAIT MARKERS
M 1 1000 1001 M 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 1 1000 1001 M 2 1 3 9 5 6 3 3 1 6
*
M 1001 -- -- M 1 3 3 9 4 6 4 4 5 6
+ ---------------------------------
P 1001 -- -- M 1 1 3 9 5 6 3 3 1 6
M 1000 2001 2002 F 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 1000 2001 2002 F 2 1 4 10 2 1 7 3 6 7
M 100 1000 1001 M 1 1 4 10 2 1 7 3 6 7
+ --------------V-------V----------
P 100 1000 1001 M 1 1 3 9 5 6 4 3 1 6
M 2002 -- -- M 1 1 4 10 2 1 7 3 6 7
+ ---------------------------------
P 2002 -- -- M 1 1 1 9 2 5 5 4 4 4
M 2001 -- -- F -- 2 5 7 2 1 10 4 5 4
+ ------------------------=-------=
P 2001 -- -- F -- 3 6 10 3 2 7 2 3 4
M 1002 2001 2002 M 1 2 5 7 2 1 10 4 5 4
+ ---------------------------------
P 1002 2001 2002 M 1 1 4 10 2 1 7 3 6 7
M 1006 2001 2002 F 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 1006 2001 2002 F 2 1 4 10 2 1 7 3 6 7
M 1007 -- -- M 1 3 6 8 3 @ 7 4 6 3
+ ---------------------------------
P 1007 -- -- M 1 3 4 1 2 6 4 2 3 4
M 1008 2001 2002 F 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 1008 2001 2002 F 2 1 1 9 2 5 5 4 4 4
M 1009 -- -- M 1 1 3 9 2 1 4 2 5 1
+ ---------------------------------
P 1009 -- -- M 1 2 3 2 3 1 5 1 2 2
M 199 -- -- F 1 @ @ 10 4 5 9 @ 4 @
+ ---------------------------------
P 199 -- -- F 1 @ @ 9 3 2 4 @ 4 @
M 1010 2001 2002 F 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 1010 2001 2002 F 2 1 1 9 2 5 5 4 4 4
M 1011 -- -- M 1 3 2 9 3 1 4 1 3 4
+ =-------=---=-------------------=
P 1011 -- -- M 1 3 4 8 3 6 5 4 4 4
M 102 1000 1001 M 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 102 1000 1001 M 2 3 3 9 4 6 4 4 5 6
M 103 -- -- F 1 2 2 10 4 6 4 3 4 6
+ --------------------------------=
P 103 -- -- F 1 1 3 10 3 6 3 1 6 4
M 104 -- -- F 1 1 4 9 3 6 5 1 7 6
+ ---------------------------------
P 104 -- -- F 1 3 3 9 2 6 10 1 8 3
M 113 1006 1007 F 2 3 6 10 3 1 7 3 6 7
+ --------------^------------------
P 113 1006 1007 F 2 3 4 1 2 6 4 2 3 4
* * *
M 114 1006 1007 F 2 3 6 10 3 2 7 2 3 4
+ --------------V------------------
P 114 1006 1007 F 2 3 6 8 3 6 4 2 3 4
M 115 1008 1009 M 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 115 1008 1009 M 2 1 3 9 2 1 4 2 5 1
*
M 116 1010 1011 M 2 3 6 10 3 2 7 2 3 4
+ ---------------------------------
P 116 1010 1011 M 2 3 2 9 3 1 4 1 3 4
M 117 1010 1011 F 1 1 1 9 2 5 5 4 4 4
+ ---------------------------------
P 117 1010 1011 F 1 3 4 8 3 6 5 4 4 4
M 9099 199 100 M 1 @ @ 9 3 2 4 @ 4 @
+ ----=---------------------------=
P 9099 199 100 M 1 1 3 9 5 6 4 3 1 6
M 9098 199 100 F -- @ @ 10 4 5 9 @ 4 @
+ ----=---------------------------=
P 9098 199 100 F -- 1 4 10 2 1 7 3 6 7
M 9097 199 100 M 1 @ @ 9 3 2 4 @ 4 @
+ ----=---------------------------=
P 9097 199 100 M 1 1 3 9 5 6 4 3 1 6
M 9003 103 102 M 2 2 2 10 4 6 4 3 4 6
+ ---------------------------------
P 9003 103 102 M 2 3 6 10 3 2 7 2 3 4
* *
M 9004 103 102 M 1 1 3 10 3 6 3 1 6 4
+ --------------V------------------
P 9004 103 102 M 1 3 6 10 3 6 4 4 5 6
*
M 9005 104 1 F 2 1 4 9 3 6 5 1 7 6
+ ---------------------------------
P 9005 104 1 F 2 3 6 10 3 2 7 2 3 4
*
M 9006 104 1 M -- 1 4 9 3 6 5 1 7 6
+ ----------------------------=---=
P 9006 104 1 M -- 1 3 9 5 6 3 3 1 6
________________________________________________________________________________
The above haplotype vector uses the actual allele names within the haplotype
representation. There is an option to instead use labels indicating from which
founder haplotype an allele is descended; with this option the allele flow
through the pedigree is even easier to see. Of course the actual allele names
associated with the labels are also provided. This option is batch item #46.2.
The above haplotype vector lists for each individual, in order: the letter
M or P indicating whether this line is their maternal or paternal haplotype,
the individual's name, their mother's name, their father's name, their sex,
and their trait phenotype, if any. The haplotype is then listed horizontally.
@ is used as the allele name when there is no information in this haplotype
vector to determine which allele is in that locus at that individual.
This occurs when a founder allele's descent through the pedigree does not
place it in any typed locus; this allele slot can be filled by ANY ALLELE.
If one must choose an allele, then the maximum likelihood solution is to
place into this slot the allele with largest frequency at that marker
(this option can be implemented using batch item #46.3).
Separating the maternal and paternal haplotypes is a line of symbols:
- is the default symbol;
^ indicates recombination in this interval only in the maternal haplotype
(this symbol points towards the marker interval on the maternal haplotype);
V indicates recombination in this interval only in the paternal haplotype
(this symbol points towards the marker interval on the paternal haplotype);
| indicates recombination in both maternal and paternal haplotypes.
= highlights maternal or paternal alleles which have been inferred.
That is, these alleles were originally undetermined but in this
haplotype vector are identical-by-descent to alleles which are known.
(This symbol is not applied to untyped alleles that are unambiguously
determined by the other alleles which are typed within the pedigree data.)
* marks those non-founder ordered genotypes whose phase is not fixed in this
haplotype vector; however, the largest likelihood was found using the phase
shown above. Of course, phase is also not fixed at any heterozygous founder
genotype. This symbol is displayed outside the genotype's paternal allele.
Batch item #46.1 gives the option of listing these haplotypes vertically.
This may be more convenient for viewing large numbers of marker loci.
As mentioned above, for non-founders, the maternal haplotype is listed first,
the paternal second. For founders, although the order is arbitrary,
when refering to the haplotype that is listed first, we again use the
term 'maternal'; the second haplotype is again called the 'paternal'.
Information on EACH RECOMBINANT:
RUN PED PEDIGREE PERSON HAPLOTYPE INTERVAL INTERVAL SIZE
NUM NUM NAME NAME ORIGIN NUMBER in Haldane cM
11 001 20 100 paternal 4 3.094
11 001 20 100 paternal 6 1.010
11 001 20 113 maternal 4 3.094
11 001 20 114 paternal 4 3.094
11 001 20 9004 paternal 4 3.094
The NUMBER OF RECOMBINANTS on each haplotype
[and the likelihood ratio of the recombination events vs. no recombination]
{and the minimum distance (in Haldane cM) between any TWO of the crossovers}:
RUN PED PEDIGREE PERSON ON THE MATERNAL ON THE PATERNAL
NUM NUM NAME NAME HAPLOTYPE HAPLOTYPE
11 001 20 100 0 [ ] { } 2 [0.000312] { 1.010}
11 001 20 113 1 [0.030928] { } 0 [ ] { }
11 001 20 114 0 [ ] { } 1 [0.030928] { }
11 001 20 9004 0 [ ] { } 1 [0.030928] { }
Summary Table:
RUN PED PED STEPS LOG-10 RECOMBINATIONS HAPLOTYPES WITH r RECOMB:
NUM NUM NAME TAKEN LIKELIHOOD EXPECTED SEEN r=0 r=1 r=2 r=3 r>3
11 001 20 48% -147.38625 4.8 5 54 3 1 0 0
This haplotype vector was found without regard to the trait locus.
The above pedigree was found on step number: 2029569
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