////////////////////////////////////////////////////////////////////
RUN NUMBER 1 (24/08/09 at 17:59:28)
////////////////////////////////////////////////////////////////////
Project information:
--------------------
NbSamples = 1
DataType = DNA
GenotypicData = 1
GameticPhase = 0
RecessiveData = 0
==============================
Settings used for Calculations
==============================
General settings:
-----------------
Deletion Weight = 1
Transition Weight Weight = 1
Tranversion Weight Weight = 1
Epsilon Value = 1e-07
Significant digits for output = 5
Use original haplotype definition
Alllowed level of missing data = 0.05
Active Tasks:
-------------
Haplotypic Frequency estimation:
--------------------------------
Make estimations at the:
Haplotypic level
Initial Conditions = 50
Maximum No. Of Iterations = 1000
Bootstrap Replicates = 0
Initial Conditions for Bootstrap = 10
No recessive Data
Do not Compact Haplotypes
==============================================================================
== ANALYSES AT THE INTRA-POPULATION LEVEL
==============================================================================
===============================================================================
== Sample : World
===============================================================================
====================================
== Haplotypes frequency estimation : (World)
====================================
Reference: Dempster, A., N. Laird and D. Rubin, 1977.
Excoffier, L. and M. Slatkin. 1995.
Lange, K., 1997.
Weir, B. S., 1996.
Excoffier, L., Laval, G., and Balding, 2004.
----------------------------------
Zipper version of the EM algorithm
----------------------------------
No. of gene copies in sample : 40
No. of random initial conditions for EM : 50
No. of different maximum likelihoods found : 2
Epsilon value for stopping iterations : 1.000000e-07
Window size for zipper EM : 1
Number or loci order : 1
Loci within window : 1 2 3 4 5 6 7 8 9 10
LogLhood : -102.2356623
------------------------------------------
Maximum-likelihood haplotype frequencies :
------------------------------------------
Total number of possible haplotypes : 203
Minimum frequency to reach for output : 1.00e-05
---------------------------------------
# Haplotype Freq. s.d.
---------------------------------------
1 UNKNOWN 0.025000 0.000000 CAAAAGGCAT
2 UNKNOWN 0.025000 0.000000 CAATACGCAT
3 UNKNOWN 0.025000 0.000000 CAATACTCAT
4 UNKNOWN 0.028229 0.000000 CGAAACGCAT
5 UNKNOWN 0.025000 0.000000 CGAAACGCCT
6 UNKNOWN 0.021771 0.000000 CGGAACTCAT
7 UNKNOWN 0.050000 0.000000 CGGTACGCAT
8 UNKNOWN 0.025000 0.000000 CGGTCGGTCT
9 UNKNOWN 0.100000 0.000000 TAATACGCAT
10 UNKNOWN 0.025000 0.000000 TAATACTCAA
11 UNKNOWN 0.050000 0.000000 TAATCGTCAT
12 UNKNOWN 0.050000 0.000000 TAGAAGGTCT
13 UNKNOWN 0.025000 0.000000 TGAAACGCAT
14 UNKNOWN 0.246771 0.000000 TGATACGCAT
15 UNKNOWN 0.050000 0.000000 TGATACGTCT
16 UNKNOWN 0.025000 0.000000 TGATACTCAT
17 UNKNOWN 0.025000 0.000000 TGATAGGCAT
18 UNKNOWN 0.025000 0.000000 TGATAGGTAT
19 UNKNOWN 0.025000 0.000000 TGATCCATAT
20 UNKNOWN 0.050000 0.000000 TGATCGGCAT
21 UNKNOWN 0.025000 0.000000 TGGACCGCAT
22 UNKNOWN 0.028229 0.000000 TGGTACTCAT
23 UNKNOWN 0.025000 0.000000 TGGTAGGTAT
---------------------------------------
Sum of all 203 haplotype frequencies : 1.000000
Sum of 23 listed frequencies : 1.000000
//------------------------------------------------------
-------------------------------------------
Maximum-likelihood frequencies of genotypes
-------------------------------------------
(Haplotypes that are not listed above have a negative id)
================
Phenotype # 1
================
Name Abs. Freq. Rel. Freq.
sample1 1 0.012339
List of genotypes ( 6)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.012339 1 CAAAAGGCAT
14 TGATACGCAT
================
Phenotype # 2
================
Name Abs. Freq. Rel. Freq.
sample2 1 0.024677
List of genotypes ( 2)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.024677 14 TGATACGCAT
20 TGATCGGCAT
================
Phenotype # 3
================
Name Abs. Freq. Rel. Freq.
sample3 1 0.012339
List of genotypes ( 5)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 0.870829 0.010745 6 CGGAACTCAT
14 TGATACGCAT
2 0.129171 0.001594 4 CGAAACGCAT
22 TGGTACTCAT
================
Phenotype # 4
================
Name Abs. Freq. Rel. Freq.
sample4 1 0.012339
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.012339 13 TGAAACGCAT
14 TGATACGCAT
================
Phenotype # 5
================
Name Abs. Freq. Rel. Freq.
sample5 1 0.002500
List of genotypes ( 2)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.002500 8 CGGTCGGTCT
20 TGATCGGCAT
================
Phenotype # 6
================
Name Abs. Freq. Rel. Freq.
sample6 1 0.012339
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.012339 14 TGATACGCAT
17 TGATAGGCAT
================
Phenotype # 7
================
Name Abs. Freq. Rel. Freq.
sample7 1 0.049354
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.049354 9 TAATACGCAT
14 TGATACGCAT
================
Phenotype # 8
================
Name Abs. Freq. Rel. Freq.
sample8 1 0.005000
List of genotypes ( 2)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.005000 9 TAATACGCAT
10 TAATACTCAA
================
Phenotype # 9
================
Name Abs. Freq. Rel. Freq.
sample9 1 0.002500
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.002500 7 CGGTACGCAT
7 CGGTACGCAT
================
Phenotype # 10
================
Name Abs. Freq. Rel. Freq.
sample10 1 0.060896
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.060896 14 TGATACGCAT
14 TGATACGCAT
================
Phenotype # 11
================
Name Abs. Freq. Rel. Freq.
sample11 1 0.001411
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.001411 4 CGAAACGCAT
5 CGAAACGCCT
================
Phenotype # 12
================
Name Abs. Freq. Rel. Freq.
sample12 1 0.010000
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.010000 9 TAATACGCAT
9 TAATACGCAT
================
Phenotype # 13
================
Name Abs. Freq. Rel. Freq.
sample13 1 0.012339
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.012339 14 TGATACGCAT
19 TGATCCATAT
================
Phenotype # 14
================
Name Abs. Freq. Rel. Freq.
sample14 1 0.001250
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.001250 18 TGATAGGTAT
23 TGGTAGGTAT
================
Phenotype # 15
================
Name Abs. Freq. Rel. Freq.
sample15 1 0.001250
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.001250 2 CAATACGCAT
3 CAATACTCAT
================
Phenotype # 16
================
Name Abs. Freq. Rel. Freq.
sample16 1 0.002500
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.002500 11 TAATCGTCAT
11 TAATCGTCAT
================
Phenotype # 17
================
Name Abs. Freq. Rel. Freq.
sample17 1 0.001411
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.001411 16 TGATACTCAT
22 TGGTACTCAT
================
Phenotype # 18
================
Name Abs. Freq. Rel. Freq.
sample18 1 0.002500
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.002500 12 TAGAAGGTCT
12 TAGAAGGTCT
================
Phenotype # 19
================
Name Abs. Freq. Rel. Freq.
sample19 1 0.002500
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.002500 15 TGATACGTCT
15 TGATACGTCT
================
Phenotype # 20
================
Name Abs. Freq. Rel. Freq.
sample20 1 0.012339
List of genotypes ( 1)
-------------------------
Gen. # Rel. Freq. Exp. Freq. Hapl. IDs Haplotypes
1 1.000000 0.012339 14 TGATACGCAT
21 TGGACCGCAT
================================================================================
== Summary of computations done within populations
================================================================================
////////////////////////////////////////////////////////////////////
END OF RUN NUMBER 1 (24/08/09 at 17:59:29))
Total computing time for this run : 0h 0m 0s 390 ms
////////////////////////////////////////////////////////////////////