################################################################ ## The Program will do: ## Input the data from file test-data-set.dat; ## Infer the haplotypes by logic rules; ## Don't perform the heuristic algorithm; ## Don't perform the haplotype elimination algorithm; ## Estimate haplotype frequencies using the PL-EM algorithm; ## List haplotype configurations with their posterior probabilities; ## Output the results to file Test-Output-00.dat; ################################################################ ################################################################ ## The following results list haplotypes and genotypes for each individual in 5 lines ## Line 1: the family ID, individual ID, father ID, mother ID, gender, and disease status ## Line 2 and Line 3: two haplotypes carried by each individual ## the symbols "a", "f", and "m" represent this haplotype is anonymous, from father, or from mother ## the haplotype can be complete or partial, in which the missing data (unassigned allele) ## is represented by "0" or "-1". However, if "-1" is in one of the haplotype, it must appear ## in the other haplotype and the genotype for this individual at this locus is complete and heterozygous ## Line 3 and 4: the genotype of this individual as a comparison ## the genotype may be different from the original because some imputations could be made ## in the genotype, the symbol "0" represents the missing data ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ The haplotypes obtained by the logic rules are: 1 1 0 0 1 0 a: 2 2 2 2 2 2 2 1 1 1 a: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 1 2 0 0 2 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 1 1 1 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 1 1 1 1 1 2 2 2 2 2 1 3 1 2 1 0 f: 2 2 2 2 2 2 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 2 1 1 1 1 2 2 1 1 1 g: 1 2 2 2 2 1 2 1 1 1 1 4 0 0 1 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 2 1 1 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 1 1 2 1 1 2 2 2 2 2 1 5 1 2 2 0 f: 2 2 2 2 2 2 1 2 2 2 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 1 6 1 2 2 0 f: 2 2 2 2 2 2 2 1 1 1 m: 1 1 1 1 1 2 1 2 2 2 g: 1 2 1 1 1 2 1 1 1 1 g: 2 1 2 2 2 2 2 2 2 2 1 7 1 2 2 0 f: 2 2 2 2 2 2 1 2 2 2 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 1 8 1 2 2 0 f: 2 2 2 2 2 2 2 1 1 1 m: 1 1 1 1 1 2 1 2 2 2 g: 1 1 1 1 1 2 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 1 9 4 5 2 0 f: 1 1 1 1 1 1 2 1 1 1 m: 2 2 2 2 2 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 1 10 4 5 2 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 4 1 0 0 1 0 a: 0 0 0 0 0 2 1 2 2 2 a: 0 0 0 0 0 0 0 0 0 0 g: 1 1 1 1 1 2 1 2 2 2 g: 0 0 0 0 0 0 0 0 0 0 4 2 0 0 2 0 a: 0 0 0 0 0 2 1 2 2 2 a: 0 0 0 0 0 0 0 0 0 0 g: 1 1 1 1 1 2 1 2 2 2 g: 0 0 0 0 0 0 0 0 0 0 4 3 1 2 1 0 a: 2 2 2 2 2 2 1 2 2 2 a: 0 1 1 1 1 2 1 2 2 2 g: 2 1 1 1 1 2 1 2 2 2 g: 0 2 2 2 2 2 1 2 2 2 4 4 0 0 2 0 a: 2 2 2 2 2 2 1 2 2 2 a: 1 1 2 1 1 2 1 2 2 2 g: 1 1 2 1 1 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 5 1 2 1 0 a: 2 2 2 2 2 2 1 2 2 2 a: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 4 6 0 0 2 0 a: 2 2 2 2 2 2 1 2 2 2 a: 2 2 2 2 0 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 0 2 1 2 2 2 4 7 1 2 1 0 a: 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 a: 2 -1 -1 -1 -1 -1 -1 -1 -1 -1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 4 8 0 0 1 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 0 1 0 1 2 1 1 2 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 0 1 0 1 2 1 1 2 4 9 1 2 2 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 1 1 1 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 1 1 1 1 1 2 2 2 2 2 4 10 3 4 2 0 f: 2 2 2 2 2 2 1 2 2 2 m: 1 1 2 1 1 2 1 2 2 2 g: 1 1 2 1 1 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 11 3 4 2 0 f: 2 2 2 2 2 2 1 2 2 2 m: 1 1 2 1 1 2 1 2 2 2 g: 1 1 2 1 1 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 12 3 4 2 0 f: 2 2 2 2 2 2 1 2 2 2 m: 1 1 2 1 1 2 1 2 2 2 g: 1 1 2 1 1 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 13 3 4 1 0 f: 2 2 2 2 2 2 1 2 2 2 m: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 14 5 6 1 0 f: 2 2 2 2 2 2 1 2 2 2 m: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 4 15 5 6 2 0 f: 1 1 1 1 1 1 2 1 1 1 m: 2 2 2 2 2 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 4 16 8 9 1 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 4 17 8 9 1 0 f: 1 1 0 1 0 1 2 1 1 0 m: 1 1 1 1 1 0 0 0 0 0 g: 1 1 1 1 1 1 2 1 1 0 g: 1 1 0 1 0 0 0 0 0 0 4 18 8 9 1 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 1 1 1 1 1 2 2 2 2 2 5 7 0 0 2 0 a: 2 2 2 2 2 2 1 2 2 2 a: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 g: 2 2 2 2 2 2 1 2 2 2 6 10 0 0 1 0 a: 1 0 1 -1 0 -1 -1 -1 -1 -1 a: 1 0 2 -1 0 -1 -1 -1 -1 -1 g: 1 0 1 1 0 1 1 1 1 1 g: 1 0 2 2 0 2 2 2 2 2 7 10 0 0 2 0 a: 0 1 -1 -1 -1 2 1 2 2 2 a: 0 2 -1 -1 -1 2 1 2 2 2 g: 0 1 1 1 1 2 1 2 2 2 g: 0 2 2 2 2 2 1 2 2 2 8 1 0 0 1 0 a: -1 2 2 2 2 2 1 2 2 2 a: -1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 8 2 0 0 2 0 a: 0 0 0 0 0 0 0 0 0 0 a: 0 0 0 0 0 0 0 0 0 0 g: 0 2 2 2 2 2 1 2 2 2 g: 0 0 0 0 0 0 0 0 0 0 8 3 1 2 2 0 a: -1 2 2 2 2 2 1 2 2 2 a: -1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 8 4 1 2 1 0 a: -1 2 2 2 2 2 1 2 2 2 a: -1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 8 5 0 0 2 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 8 6 1 2 1 0 a: 1 1 1 1 1 1 2 1 1 1 a: 2 2 2 2 2 2 1 2 2 2 g: 1 1 1 1 1 1 1 1 1 1 g: 2 2 2 2 2 2 2 2 2 2 8 7 1 2 1 0 f: 0 2 2 2 2 2 1 2 2 2 m: 0 2 2 2 2 2 1 2 2 2 g: 0 2 2 2 2 2 1 2 2 2 g: 0 2 2 2 2 2 1 2 2 2 8 8 6 5 1 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 8 9 6 5 1 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 8 10 6 5 2 0 f: 1 1 1 1 1 1 2 1 1 1 m: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 9 3 0 0 2 0 a: 1 1 1 1 1 1 2 1 1 1 a: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 g: 1 1 1 1 1 1 2 1 1 1 ################################################################ ## The following results list all compatible haplotype pairs for each individual ## Line 1: the family ID, individual ID, father ID, mother ID, gender, and disease status ## Line 2: the total number of compatible haplotype pairs for this individual ## Line 3 and ...: one of compatible haplotype pairs for this individual ## only the codes of haplotypes are given and their origins are not distinguished ## so the haplotype pairs (1,2) and (2,1) are considered as same pairs ## the corresponding haplotypes and their frequencies or counts are given at the end of this part ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ The haplotypes obtained by the PL-EM Algorithm are: 1 1 0 0 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 2 1 2 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 3 4 1 3 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 2 4 1 4 0 0 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 5 1 5 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 1 6 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 2 3 1 7 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 1 8 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 2 3 1 9 4 5 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 1 10 4 5 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 4 1 0 0 1 0 Total number of haplotype pairs is: 3 Haplotype Pair 1 is: 1 3 Haplotype Pair 2 is: 1 4 Haplotype Pair 3 is: 3 4 4 2 0 0 2 0 Total number of haplotype pairs is: 3 Haplotype Pair 1 is: 1 3 Haplotype Pair 2 is: 1 4 Haplotype Pair 3 is: 3 4 4 3 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 3 4 4 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 5 4 5 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 4 6 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 1 4 7 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 4 8 0 0 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 6 4 9 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 3 4 4 10 3 4 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 5 4 11 3 4 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 5 4 12 3 4 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 5 4 13 3 4 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 1 4 14 5 6 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 1 4 15 5 6 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 4 16 8 9 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 4 17 8 9 1 0 Total number of haplotype pairs is: 4 Haplotype Pair 1 is: 3 4 Haplotype Pair 2 is: 3 6 Haplotype Pair 3 is: 4 4 Haplotype Pair 4 is: 4 6 4 18 8 9 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 3 4 5 7 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 1 6 10 0 0 1 0 Total number of haplotype pairs is: 2 Haplotype Pair 1 is: 4 7 Haplotype Pair 2 is: 4 8 7 10 0 0 2 0 Total number of haplotype pairs is: 2 Haplotype Pair 1 is: 3 8 Haplotype Pair 2 is: 1 3 8 1 0 0 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 8 2 0 0 2 0 Total number of haplotype pairs is: 9 Haplotype Pair 1 is: 1 7 Haplotype Pair 2 is: 1 8 Haplotype Pair 3 is: 4 8 Haplotype Pair 4 is: 1 1 Haplotype Pair 5 is: 1 2 Haplotype Pair 6 is: 1 5 Haplotype Pair 7 is: 1 3 Haplotype Pair 8 is: 1 4 Haplotype Pair 9 is: 1 6 8 3 1 2 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 8 4 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 8 5 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 8 6 1 2 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 1 4 8 7 1 2 1 0 Total number of haplotype pairs is: 2 Haplotype Pair 1 is: 1 8 Haplotype Pair 2 is: 1 1 8 8 6 5 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 8 9 6 5 1 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 8 10 6 5 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 9 3 0 0 2 0 Total number of haplotype pairs is: 1 Haplotype Pair 1 is: 4 4 ################################################################ ## The following results list all haplotypes and their frequencies or counts ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ The total of 8 haplotypes are: haplotype 1 : 2 2 2 2 2 2 1 2 2 2 0.360140859 haplotype 2 : 2 2 2 2 2 2 2 1 1 1 0.033515189 haplotype 3 : 1 1 1 1 1 2 1 2 2 2 0.104782283 haplotype 4 : 1 1 1 1 1 1 2 1 1 1 0.363972572 haplotype 5 : 1 1 2 1 1 2 1 2 2 2 0.067030378 haplotype 6 : 1 1 1 1 1 1 2 1 1 2 0.033515189 haplotype 7 : 1 1 2 2 2 2 1 2 2 2 0.000038927 haplotype 8 : 1 2 2 2 2 2 1 2 2 2 0.037004604 ################################################################ ## The following results list all compatible haplotype configurations for each family ## Line 1: the family ID ## Line 2: the number of compatible haplotype configurations for this pairs family ## Line 3: the number of individuals in this family ## Line 4: the number of founders in this family ## Line 5: the number of non-founders in this family ## Line 6: the individual ID, this order is consistent with haplotype configurations in subsequent lines ## Line 7 and ...: a compatible haplotype configuration with its posterior probability ## the haplotype pair of each individual is listed ## only the codes of haplotypes are given ## the corresponding haplotypes and their frequencies are given at the endof this part ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ All compatible haplotype configurations are: Family ID is: 1 The number of haplotype configurations in this family is: 1 The number of individuals in this family is: 10 The number of founders in this family is: 3 The number of non-founders in this family is: 7 ConfigID 1 2 4 3 5 6 7 8 9 10 1 ( 1, 2) ( 3, 4) ( 4, 5) ( 2, 4) ( 1, 4) ( 2, 3) ( 1, 4) ( 2, 3) ( 1, 4) ( 4, 4) 1.000000000 Family ID is: 4 The number of haplotype configurations in this family is: 24 The number of individuals in this family is: 18 The number of founders in this family is: 5 The number of non-founders in this family is: 13 ConfigID 1 2 4 6 8 3 5 7 9 10 11 12 13 14 15 16 17 18 1 ( 1, 3) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.054310339 2 ( 1, 3) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.054310339 3 ( 1, 3) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.054310339 4 ( 1, 3) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.054310339 5 ( 1, 3) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.015801488 6 ( 1, 3) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.015801488 7 ( 1, 3) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.015801488 8 ( 1, 3) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.015801488 9 ( 1, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.054310339 10 ( 1, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.054310339 11 ( 1, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.054310339 12 ( 1, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.054310339 13 ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.054888173 14 ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.054888173 15 ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.054888173 16 ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.054888173 17 ( 3, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.015801488 18 ( 3, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.015801488 19 ( 3, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.015801488 20 ( 3, 4) ( 1, 3) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.015801488 21 ( 3, 4) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 4) ( 3, 4) 0.054888173 22 ( 3, 4) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 3, 6) ( 3, 4) 0.054888173 23 ( 3, 4) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 4) ( 3, 4) 0.054888173 24 ( 3, 4) ( 1, 4) ( 1, 5) ( 1, 1) ( 4, 6) ( 1, 3) ( 1, 4) ( 1, 4) ( 3, 4) ( 1, 5) ( 1, 5) ( 1, 5) ( 1, 1) ( 1, 1) ( 1, 4) ( 4, 4) ( 4, 6) ( 3, 4) 0.054888173 Family ID is: 5 The number of haplotype configurations in this family is: 1 The number of individuals in this family is: 1 The number of founders in this family is: 1 The number of non-founders in this family is: 0 ConfigID 7 1 ( 1, 1) 1.000000000 Family ID is: 6 The number of haplotype configurations in this family is: 2 The number of individuals in this family is: 1 The number of founders in this family is: 1 The number of non-founders in this family is: 0 ConfigID 10 1 ( 4, 7) 0.001050856 2 ( 4, 8) 0.998949144 Family ID is: 7 The number of haplotype configurations in this family is: 2 The number of individuals in this family is: 1 The number of founders in this family is: 1 The number of non-founders in this family is: 0 ConfigID 10 1 ( 3, 8) 0.093176449 2 ( 1, 3) 0.906823551 Family ID is: 8 The number of haplotype configurations in this family is: 10 The number of individuals in this family is: 10 The number of founders in this family is: 3 The number of non-founders in this family is: 7 ConfigID 1 2 5 3 4 6 7 8 9 10 1 ( 1, 4) ( 1, 7) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.000006337 2 ( 1, 4) ( 1, 8) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 8) ( 4, 4) ( 4, 4) ( 4, 4) 0.006023672 3 ( 1, 4) ( 1, 8) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.006023672 4 ( 1, 4) ( 4, 8) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 8) ( 4, 4) ( 4, 4) ( 4, 4) 0.006087761 5 ( 1, 4) ( 1, 1) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.468994711 6 ( 1, 4) ( 1, 2) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.005455659 7 ( 1, 4) ( 1, 5) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.010911318 8 ( 1, 4) ( 1, 3) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.017056637 9 ( 1, 4) ( 1, 4) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.473984573 10 ( 1, 4) ( 1, 6) ( 4, 4) ( 1, 4) ( 1, 4) ( 1, 4) ( 1, 1) ( 4, 4) ( 4, 4) ( 4, 4) 0.005455659 Family ID is: 9 The number of haplotype configurations in this family is: 1 The number of individuals in this family is: 1 The number of founders in this family is: 1 The number of non-founders in this family is: 0 ConfigID 3 1 ( 4, 4) 1.000000000 ################################################################ ## The following results list all haplotypes and their frequencies or counts ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ The total of 8 haplotypes are: haplotype 1 : 2 2 2 2 2 2 1 2 2 2 0.360140859 haplotype 2 : 2 2 2 2 2 2 2 1 1 1 0.033515189 haplotype 3 : 1 1 1 1 1 2 1 2 2 2 0.104782283 haplotype 4 : 1 1 1 1 1 1 2 1 1 1 0.363972572 haplotype 5 : 1 1 2 1 1 2 1 2 2 2 0.067030378 haplotype 6 : 1 1 1 1 1 1 2 1 1 2 0.033515189 haplotype 7 : 1 1 2 2 2 2 1 2 2 2 0.000038927 haplotype 8 : 1 2 2 2 2 2 1 2 2 2 0.037004604 ################################################################ ## The following results list the haplotype configuration with the maximum probability in each family ## Each individual takes one line with 10 columns: ## Column 1: the family ID of this individual ## Column 2: the individual ID of this individual ## Column 3: the father ID of this individual ## Column 4: the mother ID of this individual ## Column 5: the gender of this individual ## Column 6: the disease status of this individual ## Column 7: the first haplotype, which is coded as an allele at a multi-allelic locus ## Column 8: the second haplotype, which is coded as an allele at a multi-allelic locus ## Column 9: the first haplotype with alleles at marker loci ## Column 10: the second haplotype with alleles at marker loci ## ATTENTION: PLEASE REFER to the HELP FILE for MORE DETAILS!!! ################################################################ 1 1 0 0 1 0 1 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 0 0 2 0 3 4 1 1 1 1 1 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 4 0 0 1 0 4 5 1 1 1 1 1 1 2 1 1 1 1 1 2 1 1 2 1 2 2 2 1 3 1 2 1 0 2 4 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 5 1 2 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 6 1 2 2 0 2 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 2 1 2 2 2 1 7 1 2 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 8 1 2 2 0 2 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 2 1 2 2 2 1 9 4 5 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 1 10 4 5 2 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 4 1 0 0 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 2 0 0 2 0 3 4 1 1 1 1 1 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 4 0 0 2 0 1 5 2 2 2 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 2 2 4 6 0 0 2 0 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 2 4 8 0 0 1 0 4 6 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 4 3 1 2 1 0 1 3 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 2 1 2 2 2 4 5 1 2 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 7 1 2 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 9 1 2 2 0 3 4 1 1 1 1 1 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 10 3 4 2 0 1 5 2 2 2 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 2 2 4 11 3 4 2 0 1 5 2 2 2 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 2 2 4 12 3 4 2 0 1 5 2 2 2 2 2 2 1 2 2 2 1 1 2 1 1 2 1 2 2 2 4 13 3 4 1 0 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 2 4 14 5 6 1 0 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 2 4 15 5 6 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 16 8 9 1 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 4 17 8 9 1 0 3 4 1 1 1 1 1 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 4 18 8 9 1 0 3 4 1 1 1 1 1 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 5 7 0 0 2 0 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 2 6 10 0 0 1 0 4 8 1 1 1 1 1 1 2 1 1 1 1 2 2 2 2 2 1 2 2 2 7 10 0 0 2 0 1 3 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 2 1 2 2 2 8 1 0 0 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 8 2 0 0 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 8 5 0 0 2 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 8 3 1 2 2 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 8 4 1 2 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 8 6 1 2 1 0 1 4 2 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 2 1 1 1 8 7 1 2 1 0 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 2 8 8 6 5 1 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 8 9 6 5 1 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 8 10 6 5 2 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 9 3 0 0 2 0 4 4 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1