File fam19_0 passed to main function.

command: /home/cbardel/FAMHAP/FAMHAP15/famhap15 fam19_0 trio.fmh dp P 

Input seems to have no column headings. Program proceeds.
Infile has 26 columns. It is assumed to have 10 marker(s).
300 individuals were read.
100 families were read.

Mendel Check successful. No distortions encountered.

The following loci were selected: 1 2 3 4 5 6 7 8 9 10 
Only families fully genotyped at these loci will be included into the frequency estimation.

independent case chromosomes: 200 control chromosomes: 200
Internal Recoding.

CODING MARKER 1.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 2.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 3.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 4.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 5.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 6.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 7.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 8.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 9.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

CODING MARKER 10.
Allele 0 Code 0
Allele 1 Code 1
Allele 2 Code 2

HAPLOTYPE ESTIMATION WITH DOUBLED PARAMETER SET:

Selected loci: 1 2 3 4 5 6 7 8 9 10 
Number of alleles at the loci: 2 2 2 2 2 2 2 2 2 2 

Haplotype parameters at beginning (not doubled): 1024

Loglikelihood -1105.715154

9 iterations were performed.

1 1 1 1 1 2 2 2 2 1  HaploiD: 30 FreqAff 0.045000 FreqUnaff 0.015000
1 1 1 1 2 1 1 1 1 1  HaploiD: 32 FreqAff 0.000000 FreqUnaff 0.040000
1 1 1 1 2 1 2 2 2 1  HaploiD: 46 FreqAff 0.005000 FreqUnaff 0.025000
1 1 1 1 2 2 1 1 1 2  HaploiD: 49 FreqAff 0.005000 FreqUnaff 0.010000
1 1 1 1 2 2 2 1 2 1  HaploiD: 58 FreqAff 0.025000 FreqUnaff 0.050000
1 1 1 1 2 2 2 2 2 1  HaploiD: 62 FreqAff 0.005000 FreqUnaff 0.010000
1 1 2 1 1 1 1 1 1 1  HaploiD: 128 FreqAff 0.010000 FreqUnaff 0.000000
1 1 2 1 2 1 1 1 1 1  HaploiD: 160 FreqAff 0.011593 FreqUnaff 0.040833
1 1 2 1 2 1 1 1 1 2  HaploiD: 161 FreqAff 0.005373 FreqUnaff 0.014119
1 1 2 1 2 1 2 2 2 1  HaploiD: 174 FreqAff 0.128034 FreqUnaff 0.180048
1 1 2 1 2 1 2 2 2 2  HaploiD: 175 FreqAff 0.005000 FreqUnaff 0.000000
1 1 2 2 2 1 1 1 1 1  HaploiD: 224 FreqAff 0.010000 FreqUnaff 0.010000
1 1 2 2 2 1 2 2 1 1  HaploiD: 236 FreqAff 0.005000 FreqUnaff 0.005000
1 2 2 2 2 1 1 1 1 1  HaploiD: 480 FreqAff 0.126493 FreqUnaff 0.191914
1 2 2 2 2 1 1 1 1 2  HaploiD: 481 FreqAff 0.025000 FreqUnaff 0.045881
1 2 2 2 2 1 1 1 2 1  HaploiD: 482 FreqAff 0.010000 FreqUnaff 0.030000
1 2 2 2 2 1 1 2 1 1  HaploiD: 484 FreqAff 0.020000 FreqUnaff 0.000000
1 2 2 2 2 1 2 2 2 1  HaploiD: 494 FreqAff 0.108507 FreqUnaff 0.097205
2 1 1 1 1 2 2 1 2 1  HaploiD: 538 FreqAff 0.055000 FreqUnaff 0.010000
2 1 1 1 2 1 1 1 1 1  HaploiD: 544 FreqAff 0.010000 FreqUnaff 0.015000
2 1 1 1 2 1 2 2 2 1  HaploiD: 558 FreqAff 0.005000 FreqUnaff 0.000000
2 1 2 1 1 2 1 2 2 1  HaploiD: 662 FreqAff 0.000000 FreqUnaff 0.005000
2 1 2 1 1 2 2 2 2 1  HaploiD: 670 FreqAff 0.010000 FreqUnaff 0.010000
2 1 2 1 2 1 1 1 1 2  HaploiD: 673 FreqAff 0.000000 FreqUnaff 0.005000
2 1 2 2 1 1 1 1 1 2  HaploiD: 705 FreqAff 0.045000 FreqUnaff 0.005000
2 1 2 2 1 1 2 2 2 1  HaploiD: 718 FreqAff 0.055000 FreqUnaff 0.010000
2 1 2 2 1 2 1 1 1 1  HaploiD: 720 FreqAff 0.011914 FreqUnaff 0.017253
2 1 2 2 1 2 1 1 1 2  HaploiD: 721 FreqAff 0.074627 FreqUnaff 0.025000
2 1 2 2 1 2 2 1 2 1  HaploiD: 730 FreqAff 0.005000 FreqUnaff 0.000000
2 1 2 2 1 2 2 2 1 1  HaploiD: 732 FreqAff 0.005000 FreqUnaff 0.000000
2 1 2 2 1 2 2 2 2 1  HaploiD: 734 FreqAff 0.143459 FreqUnaff 0.092747
2 1 2 2 1 2 2 2 2 2  HaploiD: 735 FreqAff 0.010000 FreqUnaff 0.010000
2 1 2 2 2 1 1 1 1 1  HaploiD: 736 FreqAff 0.005000 FreqUnaff 0.015000
2 1 2 2 2 1 1 1 1 2  HaploiD: 737 FreqAff 0.005000 FreqUnaff 0.000000
2 1 2 2 2 1 2 2 2 1  HaploiD: 750 FreqAff 0.010000 FreqUnaff 0.015000

200 independent case chromosomes could be incorporated into the analysis.
200 independent control chromosomes could be incorporated into the analysis.



The following families could be incorporated into the estimation:
0 1 2 3 4 5 6 7 8 9 10 11 12 
13 14 15 16 17 18 19 20 21 22 23 24 25 
26 27 28 29 30 31 32 33 34 35 36 37 38 
39 40 41 42 43 44 45 46 47 48 49 50 51 
52 53 54 55 56 57 58 59 60 61 62 63 64 
65 66 67 68 69 70 71 72 73 74 75 76 77 
78 79 80 81 82 83 84 85 86 87 88 89 90 
91 92 93 94 95 96 97 98 99 

All families could be incorporated.


NUMBER OF PARAMETERS DIFFERENT FROM ZERO-1 = 34.

Total number of haplotype explanations:290

