This is MalHaploFreq version 2.1.0 Analysis started Wed May 26 08:28:51 2010 Now reading input parameters from file MHFparameters.txt data_type read as 2 ML_precision read as 8 CI_precision read as 3 max_clones read as 12 lose_minority_clones read as n detection_limit read as 0.300000 clonality_known read as y distribution_type read as 1 check_hillclimb read as n check_programme_accuracy read as n simulation_transmission_intensity read as n required_dataset_size read as 100 required_reps read as 1000 Starting replicate number 1 *******First to make a few internal checks on mathematical conventions ******** this system assumes 0 raised to the power 0 is 1.000000 Checking log factorials are being calculated correctly log factorial of 5 should be 4.787, programme calulates it as 4.787492 log factorial of 50 calculated as 148.477767 log factorial of 5000 calculated as 37591.143509 starting guestimate for the wildtype haplotype is 0.186669 file MHFdatafile.txt successfully opened for reading genotyping and MOI data ********* Now reading and processing record record no. 1 ******** record read as 0 0 0 3 Record 1 being included in ML analysis with data 0 0 0 3 record 1 is unambiguous at codon 1 record 1 is unambiguous at codon 2 record 1 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 2 ******** record read as 0 0 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 2 being included in ML analysis with data 0 0 0 2 record 2 is unambiguous at codon 1 record 2 is unambiguous at codon 2 record 2 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 3 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 3 being included in ML analysis with data 0 0 0 3 record 3 is unambiguous at codon 1 record 3 is unambiguous at codon 2 record 3 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 4 ******** record read as 0 1 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 4 being included in ML analysis with data 0 1 0 4 record 4 is unambiguous at codon 1 record 4 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 5 ******** record read as 0 0 0 9 Record 5 being included in ML analysis with data 0 0 0 9 record 5 is unambiguous at codon 1 record 5 is unambiguous at codon 2 record 5 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 6 ******** record read as 0 0 0 3 Record 6 being included in ML analysis with data 0 0 0 3 record 6 is unambiguous at codon 1 record 6 is unambiguous at codon 2 record 6 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 7 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 7 being included in ML analysis with data 0 0 0 2 record 7 is unambiguous at codon 1 record 7 is unambiguous at codon 2 record 7 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 8 ******** record read as 0 0 0 7 Record 8 being included in ML analysis with data 0 0 0 7 record 8 is unambiguous at codon 1 record 8 is unambiguous at codon 2 record 8 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 9 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 9 being included in ML analysis with data 0 0 0 2 record 9 is unambiguous at codon 1 record 9 is unambiguous at codon 2 record 9 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 10 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 10 being included in ML analysis with data 0 0 0 1 record 10 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 10 is unambiguous at codon 1 record 10 is unambiguous at codon 2 record 10 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 11 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 11 being included in ML analysis with data 0 0 0 2 record 11 is unambiguous at codon 1 record 11 is unambiguous at codon 2 record 11 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 12 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 12 being included in ML analysis with data 0 0 0 4 record 12 is unambiguous at codon 1 record 12 is unambiguous at codon 2 record 12 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 13 ******** record read as 0 0 0 6 Record 13 being included in ML analysis with data 0 0 0 6 record 13 is unambiguous at codon 1 record 13 is unambiguous at codon 2 record 13 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 14 ******** record read as 0 0 99 1 missing data in third codon of record 14 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 14 being included in ML analysis with data 0 0 0 1 record 14 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 14 is unambiguous at codon 1 record 14 is unambiguous at codon 2 record 14 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 15 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 15 being included in ML analysis with data 0 0 0 2 record 15 is unambiguous at codon 1 record 15 is unambiguous at codon 2 record 15 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 16 ******** record read as 1 1 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 16 being included in ML analysis with data 1 1 0 2 record 16 is unambiguous at codon 1 record 16 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because both codons are heterozygous so cannot determine linkage phase ********* Now reading and processing record record no. 17 ******** record read as 0 0 0 5 Record 17 being included in ML analysis with data 0 0 0 5 record 17 is unambiguous at codon 1 record 17 is unambiguous at codon 2 record 17 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 18 ******** record read as 0 0 0 4 Record 18 being included in ML analysis with data 0 0 0 4 record 18 is unambiguous at codon 1 record 18 is unambiguous at codon 2 record 18 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 19 ******** record read as 0 0 0 1 Record 19 being included in ML analysis with data 0 0 0 1 record 19 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 19 is unambiguous at codon 1 record 19 is unambiguous at codon 2 record 19 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 20 ******** record read as 1 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 20 being included in ML analysis with data 1 0 0 4 record 20 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 20 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 21 ******** record read as 0 0 0 7 Record 21 being included in ML analysis with data 0 0 0 7 record 21 is unambiguous at codon 1 record 21 is unambiguous at codon 2 record 21 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 22 ******** record read as 0 0 1 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 22 being included in ML analysis with data 0 0 0 6 record 22 is unambiguous at codon 1 record 22 is unambiguous at codon 2 record 22 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 23 ******** record read as 0 0 0 3 Record 23 being included in ML analysis with data 0 0 0 3 record 23 is unambiguous at codon 1 record 23 is unambiguous at codon 2 record 23 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 24 ******** record read as 0 0 0 4 Record 24 being included in ML analysis with data 0 0 0 4 record 24 is unambiguous at codon 1 record 24 is unambiguous at codon 2 record 24 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 25 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 25 being included in ML analysis with data 0 0 0 1 record 25 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 25 is unambiguous at codon 1 record 25 is unambiguous at codon 2 record 25 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 26 ******** record read as 0 0 0 4 Record 26 being included in ML analysis with data 0 0 0 4 record 26 is unambiguous at codon 1 record 26 is unambiguous at codon 2 record 26 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 27 ******** record read as 0 0 0 7 Record 27 being included in ML analysis with data 0 0 0 7 record 27 is unambiguous at codon 1 record 27 is unambiguous at codon 2 record 27 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 28 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 28 being included in ML analysis with data 0 0 0 3 record 28 is unambiguous at codon 1 record 28 is unambiguous at codon 2 record 28 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 29 ******** record read as 0 0 0 6 Record 29 being included in ML analysis with data 0 0 0 6 record 29 is unambiguous at codon 1 record 29 is unambiguous at codon 2 record 29 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 30 ******** record read as 0 0 0 6 Record 30 being included in ML analysis with data 0 0 0 6 record 30 is unambiguous at codon 1 record 30 is unambiguous at codon 2 record 30 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 31 ******** record read as 0 0 99 8 missing data in third codon of record 31 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 31 being included in ML analysis with data 0 0 0 8 record 31 is unambiguous at codon 1 record 31 is unambiguous at codon 2 record 31 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 32 ******** record read as 0 0 0 7 Record 32 being included in ML analysis with data 0 0 0 7 record 32 is unambiguous at codon 1 record 32 is unambiguous at codon 2 record 32 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 33 ******** record read as 0 0 0 4 Record 33 being included in ML analysis with data 0 0 0 4 record 33 is unambiguous at codon 1 record 33 is unambiguous at codon 2 record 33 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 34 ******** record read as 0 0 0 6 Record 34 being included in ML analysis with data 0 0 0 6 record 34 is unambiguous at codon 1 record 34 is unambiguous at codon 2 record 34 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 35 ******** record read as 0 1 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 35 being included in ML analysis with data 0 1 0 2 record 35 is unambiguous at codon 1 record 35 is unambiguous at codon 2 record 35 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 36 ******** record read as 0 0 0 5 Record 36 being included in ML analysis with data 0 0 0 5 record 36 is unambiguous at codon 1 record 36 is unambiguous at codon 2 record 36 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 37 ******** record read as 99 0 99 8 WARNING missing data in first codon of record 37 so this record will be ignored ********* Now reading and processing record record no. 38 ******** record read as 0 0 0 4 Record 38 being included in ML analysis with data 0 0 0 4 record 38 is unambiguous at codon 1 record 38 is unambiguous at codon 2 record 38 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 39 ******** record read as 0 0 99 2 missing data in third codon of record 39 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 39 being included in ML analysis with data 0 0 0 2 record 39 is unambiguous at codon 1 record 39 is unambiguous at codon 2 record 39 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 40 ******** record read as 0 0 0 8 Record 40 being included in ML analysis with data 0 0 0 8 record 40 is unambiguous at codon 1 record 40 is unambiguous at codon 2 record 40 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 41 ******** record read as 0 0 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 41 being included in ML analysis with data 0 0 0 5 record 41 is unambiguous at codon 1 record 41 is unambiguous at codon 2 record 41 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 42 ******** record read as 99 99 99 3 WARNING missing data in first codon of record 42 so this record will be ignored ********* Now reading and processing record record no. 43 ******** record read as 0 0 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 43 being included in ML analysis with data 0 0 0 5 record 43 is unambiguous at codon 1 record 43 is unambiguous at codon 2 record 43 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 44 ******** record read as 0 0 0 6 Record 44 being included in ML analysis with data 0 0 0 6 record 44 is unambiguous at codon 1 record 44 is unambiguous at codon 2 record 44 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 45 ******** record read as 0 0 99 3 missing data in third codon of record 45 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 45 being included in ML analysis with data 0 0 0 3 record 45 is unambiguous at codon 1 record 45 is unambiguous at codon 2 record 45 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 46 ******** record read as 99 0 99 1 WARNING missing data in first codon of record 46 so this record will be ignored ********* Now reading and processing record record no. 47 ******** record read as 0 0 0 2 Record 47 being included in ML analysis with data 0 0 0 2 record 47 is unambiguous at codon 1 record 47 is unambiguous at codon 2 record 47 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 48 ******** record read as 99 0 99 1 WARNING missing data in first codon of record 48 so this record will be ignored ********* Now reading and processing record record no. 49 ******** record read as 0 0 0 3 Record 49 being included in ML analysis with data 0 0 0 3 record 49 is unambiguous at codon 1 record 49 is unambiguous at codon 2 record 49 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 50 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 50 so this record will be ignored ********* Now reading and processing record record no. 51 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 51 being included in ML analysis with data 0 0 0 3 record 51 is unambiguous at codon 1 record 51 is unambiguous at codon 2 record 51 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 52 ******** record read as 0 0 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 52 being included in ML analysis with data 0 0 0 6 record 52 is unambiguous at codon 1 record 52 is unambiguous at codon 2 record 52 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 53 ******** record read as 99 0 99 2 WARNING missing data in first codon of record 53 so this record will be ignored ********* Now reading and processing record record no. 54 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 54 being included in ML analysis with data 0 0 0 4 record 54 is unambiguous at codon 1 record 54 is unambiguous at codon 2 record 54 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 55 ******** record read as 0 0 0 2 Record 55 being included in ML analysis with data 0 0 0 2 record 55 is unambiguous at codon 1 record 55 is unambiguous at codon 2 record 55 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 56 ******** record read as 0 0 0 5 Record 56 being included in ML analysis with data 0 0 0 5 record 56 is unambiguous at codon 1 record 56 is unambiguous at codon 2 record 56 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 57 ******** record read as 99 99 2 3 WARNING missing data in first codon of record 57 so this record will be ignored ********* Now reading and processing record record no. 58 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 58 so this record will be ignored ********* Now reading and processing record record no. 59 ******** record read as 0 0 99 2 missing data in third codon of record 59 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 59 being included in ML analysis with data 0 0 0 2 record 59 is unambiguous at codon 1 record 59 is unambiguous at codon 2 record 59 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 60 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 60 being included in ML analysis with data 0 0 0 3 record 60 is unambiguous at codon 1 record 60 is unambiguous at codon 2 record 60 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 61 ******** record read as 2 2 99 1 missing data in third codon of record 61 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 61 being included in ML analysis with data 2 2 0 1 record 61 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 61 is unambiguous at codon 1 record 61 is unambiguous at codon 2 record 61 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 62 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 62 being included in ML analysis with data 0 0 0 5 record 62 is unambiguous at codon 1 record 62 is unambiguous at codon 2 record 62 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 63 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 63 being included in ML analysis with data 0 0 0 3 record 63 is unambiguous at codon 1 record 63 is unambiguous at codon 2 record 63 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 64 ******** record read as 0 0 1 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 64 being included in ML analysis with data 0 0 0 4 record 64 is unambiguous at codon 1 record 64 is unambiguous at codon 2 record 64 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 65 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 65 being included in ML analysis with data 0 0 0 2 record 65 is unambiguous at codon 1 record 65 is unambiguous at codon 2 record 65 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 66 ******** record read as 0 1 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 66 being included in ML analysis with data 0 1 0 3 record 66 is unambiguous at codon 1 record 66 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 67 ******** record read as 0 0 0 3 Record 67 being included in ML analysis with data 0 0 0 3 record 67 is unambiguous at codon 1 record 67 is unambiguous at codon 2 record 67 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 68 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 68 so this record will be ignored ********* Now reading and processing record record no. 69 ******** record read as 0 0 99 6 missing data in third codon of record 69 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 69 being included in ML analysis with data 0 0 0 6 record 69 is unambiguous at codon 1 record 69 is unambiguous at codon 2 record 69 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 70 ******** record read as 2 2 99 1 missing data in third codon of record 70 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 70 being included in ML analysis with data 2 2 0 1 record 70 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 70 is unambiguous at codon 1 record 70 is unambiguous at codon 2 record 70 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 71 ******** record read as 0 1 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 71 being included in ML analysis with data 0 1 0 4 record 71 is unambiguous at codon 1 record 71 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 72 ******** record read as 0 0 1 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 72 being included in ML analysis with data 0 0 0 3 record 72 is unambiguous at codon 1 record 72 is unambiguous at codon 2 record 72 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 73 ******** record read as 0 0 99 6 missing data in third codon of record 73 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 73 being included in ML analysis with data 0 0 0 6 record 73 is unambiguous at codon 1 record 73 is unambiguous at codon 2 record 73 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 74 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 74 being included in ML analysis with data 0 0 0 2 record 74 is unambiguous at codon 1 record 74 is unambiguous at codon 2 record 74 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 75 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 75 being included in ML analysis with data 0 0 0 1 record 75 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 75 is unambiguous at codon 1 record 75 is unambiguous at codon 2 record 75 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 76 ******** record read as 99 2 2 3 WARNING missing data in first codon of record 76 so this record will be ignored ********* Now reading and processing record record no. 77 ******** record read as 0 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 77 being included in ML analysis with data 0 2 0 3 record 77 is unambiguous at codon 1 record 77 is unambiguous at codon 2 record 77 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 78 ******** record read as 0 0 99 4 missing data in third codon of record 78 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 78 being included in ML analysis with data 0 0 0 4 record 78 is unambiguous at codon 1 record 78 is unambiguous at codon 2 record 78 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 79 ******** record read as 0 1 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 79 being included in ML analysis with data 0 1 0 2 record 79 is unambiguous at codon 1 record 79 is unambiguous at codon 2 record 79 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 80 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 80 being included in ML analysis with data 0 0 0 3 record 80 is unambiguous at codon 1 record 80 is unambiguous at codon 2 record 80 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 81 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 81 being included in ML analysis with data 0 0 0 3 record 81 is unambiguous at codon 1 record 81 is unambiguous at codon 2 record 81 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 82 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 82 being included in ML analysis with data 0 0 0 3 record 82 is unambiguous at codon 1 record 82 is unambiguous at codon 2 record 82 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 83 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 83 being included in ML analysis with data 0 0 0 5 record 83 is unambiguous at codon 1 record 83 is unambiguous at codon 2 record 83 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 84 ******** record read as 0 0 0 2 Record 84 being included in ML analysis with data 0 0 0 2 record 84 is unambiguous at codon 1 record 84 is unambiguous at codon 2 record 84 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 85 ******** record read as 0 0 0 5 Record 85 being included in ML analysis with data 0 0 0 5 record 85 is unambiguous at codon 1 record 85 is unambiguous at codon 2 record 85 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 86 ******** record read as 99 99 2 5 WARNING missing data in first codon of record 86 so this record will be ignored ********* Now reading and processing record record no. 87 ******** record read as 0 0 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 87 being included in ML analysis with data 0 0 0 2 record 87 is unambiguous at codon 1 record 87 is unambiguous at codon 2 record 87 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 88 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 88 being included in ML analysis with data 0 0 0 4 record 88 is unambiguous at codon 1 record 88 is unambiguous at codon 2 record 88 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 89 ******** record read as 99 0 2 2 WARNING missing data in first codon of record 89 so this record will be ignored ********* Now reading and processing record record no. 90 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 90 being included in ML analysis with data 0 0 0 4 record 90 is unambiguous at codon 1 record 90 is unambiguous at codon 2 record 90 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 91 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 91 being included in ML analysis with data 0 0 0 3 record 91 is unambiguous at codon 1 record 91 is unambiguous at codon 2 record 91 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 92 ******** record read as 0 0 0 5 Record 92 being included in ML analysis with data 0 0 0 5 record 92 is unambiguous at codon 1 record 92 is unambiguous at codon 2 record 92 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 93 ******** record read as 99 0 0 4 WARNING missing data in first codon of record 93 so this record will be ignored ********* Now reading and processing record record no. 94 ******** record read as 0 0 0 3 Record 94 being included in ML analysis with data 0 0 0 3 record 94 is unambiguous at codon 1 record 94 is unambiguous at codon 2 record 94 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 95 ******** record read as 99 0 2 3 WARNING missing data in first codon of record 95 so this record will be ignored ********* Now reading and processing record record no. 96 ******** record read as 0 0 0 5 Record 96 being included in ML analysis with data 0 0 0 5 record 96 is unambiguous at codon 1 record 96 is unambiguous at codon 2 record 96 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 97 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 97 being included in ML analysis with data 0 0 0 5 record 97 is unambiguous at codon 1 record 97 is unambiguous at codon 2 record 97 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 98 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 98 so this record will be ignored ********* Now reading and processing record record no. 99 ******** record read as 0 0 99 5 missing data in third codon of record 99 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 99 being included in ML analysis with data 0 0 0 5 record 99 is unambiguous at codon 1 record 99 is unambiguous at codon 2 record 99 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 100 ******** record read as 2 1 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 100 being included in ML analysis with data 2 1 0 2 record 100 is unambiguous at codon 1 record 100 is unambiguous at codon 2 record 100 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 101 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 101 so this record will be ignored ********* Now reading and processing record record no. 102 ******** record read as 99 99 2 1 WARNING missing data in first codon of record 102 so this record will be ignored ********* Now reading and processing record record no. 103 ******** record read as 99 0 2 3 WARNING missing data in first codon of record 103 so this record will be ignored ********* Now reading and processing record record no. 104 ******** record read as 2 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 104 being included in ML analysis with data 2 0 0 2 record 104 is unambiguous at codon 1 record 104 is unambiguous at codon 2 record 104 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 105 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 105 being included in ML analysis with data 0 0 0 1 record 105 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 105 is unambiguous at codon 1 record 105 is unambiguous at codon 2 record 105 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 106 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 106 being included in ML analysis with data 0 0 0 3 record 106 is unambiguous at codon 1 record 106 is unambiguous at codon 2 record 106 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 107 ******** record read as 0 0 99 4 missing data in third codon of record 107 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 107 being included in ML analysis with data 0 0 0 4 record 107 is unambiguous at codon 1 record 107 is unambiguous at codon 2 record 107 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 108 ******** record read as 0 0 99 5 missing data in third codon of record 108 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 108 being included in ML analysis with data 0 0 0 5 record 108 is unambiguous at codon 1 record 108 is unambiguous at codon 2 record 108 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 109 ******** record read as 0 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 109 being included in ML analysis with data 0 2 0 3 record 109 is unambiguous at codon 1 record 109 is unambiguous at codon 2 record 109 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 110 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 110 being included in ML analysis with data 0 0 0 4 record 110 is unambiguous at codon 1 record 110 is unambiguous at codon 2 record 110 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 111 ******** record read as 2 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 111 being included in ML analysis with data 2 2 0 2 record 111 is unambiguous at codon 1 record 111 is unambiguous at codon 2 record 111 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 112 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 112 being included in ML analysis with data 0 0 0 3 record 112 is unambiguous at codon 1 record 112 is unambiguous at codon 2 record 112 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 113 ******** record read as 0 2 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 113 being included in ML analysis with data 0 2 0 4 record 113 is unambiguous at codon 1 record 113 is unambiguous at codon 2 record 113 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 114 ******** record read as 0 0 0 3 Record 114 being included in ML analysis with data 0 0 0 3 record 114 is unambiguous at codon 1 record 114 is unambiguous at codon 2 record 114 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 115 ******** record read as 0 0 0 4 Record 115 being included in ML analysis with data 0 0 0 4 record 115 is unambiguous at codon 1 record 115 is unambiguous at codon 2 record 115 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 116 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 116 being included in ML analysis with data 0 0 0 5 record 116 is unambiguous at codon 1 record 116 is unambiguous at codon 2 record 116 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 117 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 117 being included in ML analysis with data 0 0 0 2 record 117 is unambiguous at codon 1 record 117 is unambiguous at codon 2 record 117 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 118 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 118 being included in ML analysis with data 0 0 0 3 record 118 is unambiguous at codon 1 record 118 is unambiguous at codon 2 record 118 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 119 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 119 being included in ML analysis with data 0 0 0 2 record 119 is unambiguous at codon 1 record 119 is unambiguous at codon 2 record 119 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 120 ******** record read as 0 2 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 120 being included in ML analysis with data 0 2 0 7 record 120 is unambiguous at codon 1 record 120 is unambiguous at codon 2 record 120 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 121 ******** record read as 0 0 0 4 Record 121 being included in ML analysis with data 0 0 0 4 record 121 is unambiguous at codon 1 record 121 is unambiguous at codon 2 record 121 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 122 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 122 being included in ML analysis with data 0 0 0 2 record 122 is unambiguous at codon 1 record 122 is unambiguous at codon 2 record 122 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 123 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 123 being included in ML analysis with data 0 0 0 1 record 123 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 123 is unambiguous at codon 1 record 123 is unambiguous at codon 2 record 123 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 124 ******** record read as 99 99 2 6 WARNING missing data in first codon of record 124 so this record will be ignored ********* Now reading and processing record record no. 125 ******** record read as 0 0 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 125 being included in ML analysis with data 0 0 0 6 record 125 is unambiguous at codon 1 record 125 is unambiguous at codon 2 record 125 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 126 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 126 so this record will be ignored ********* Now reading and processing record record no. 127 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 127 so this record will be ignored ********* Now reading and processing record record no. 128 ******** record read as 0 0 0 1 Record 128 being included in ML analysis with data 0 0 0 1 record 128 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 128 is unambiguous at codon 1 record 128 is unambiguous at codon 2 record 128 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 129 ******** record read as 0 0 0 2 Record 129 being included in ML analysis with data 0 0 0 2 record 129 is unambiguous at codon 1 record 129 is unambiguous at codon 2 record 129 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 130 ******** record read as 0 0 0 5 Record 130 being included in ML analysis with data 0 0 0 5 record 130 is unambiguous at codon 1 record 130 is unambiguous at codon 2 record 130 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 131 ******** record read as 0 0 0 6 Record 131 being included in ML analysis with data 0 0 0 6 record 131 is unambiguous at codon 1 record 131 is unambiguous at codon 2 record 131 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 132 ******** record read as 99 0 99 7 WARNING missing data in first codon of record 132 so this record will be ignored ********* Now reading and processing record record no. 133 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 133 being included in ML analysis with data 0 0 0 5 record 133 is unambiguous at codon 1 record 133 is unambiguous at codon 2 record 133 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 134 ******** record read as 0 0 0 5 Record 134 being included in ML analysis with data 0 0 0 5 record 134 is unambiguous at codon 1 record 134 is unambiguous at codon 2 record 134 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 135 ******** record read as 0 0 1 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 135 being included in ML analysis with data 0 0 0 4 record 135 is unambiguous at codon 1 record 135 is unambiguous at codon 2 record 135 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 136 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 136 being included in ML analysis with data 0 0 0 2 record 136 is unambiguous at codon 1 record 136 is unambiguous at codon 2 record 136 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 137 ******** record read as 99 0 2 10 WARNING missing data in first codon of record 137 so this record will be ignored ********* Now reading and processing record record no. 138 ******** record read as 0 0 0 1 Record 138 being included in ML analysis with data 0 0 0 1 record 138 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 138 is unambiguous at codon 1 record 138 is unambiguous at codon 2 record 138 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 139 ******** record read as 0 0 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 139 being included in ML analysis with data 0 0 0 5 record 139 is unambiguous at codon 1 record 139 is unambiguous at codon 2 record 139 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 140 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 140 so this record will be ignored ********* Now reading and processing record record no. 141 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 141 being included in ML analysis with data 0 0 0 2 record 141 is unambiguous at codon 1 record 141 is unambiguous at codon 2 record 141 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 142 ******** record read as 99 0 2 5 WARNING missing data in first codon of record 142 so this record will be ignored ********* Now reading and processing record record no. 143 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 143 so this record will be ignored ********* Now reading and processing record record no. 144 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 144 so this record will be ignored ********* Now reading and processing record record no. 145 ******** record read as 1 1 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 145 being included in ML analysis with data 1 1 0 4 record 145 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 145 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 146 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 146 being included in ML analysis with data 0 0 0 2 record 146 is unambiguous at codon 1 record 146 is unambiguous at codon 2 record 146 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 147 ******** record read as 0 0 0 5 Record 147 being included in ML analysis with data 0 0 0 5 record 147 is unambiguous at codon 1 record 147 is unambiguous at codon 2 record 147 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 148 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 148 so this record will be ignored ********* Now reading and processing record record no. 149 ******** record read as 0 99 99 2 WARNING missing data in second codon of record 149 so this record will be ignored ********* Now reading and processing record record no. 150 ******** record read as 1 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 150 being included in ML analysis with data 1 0 0 5 record 150 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 150 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 151 ******** record read as 0 0 0 4 Record 151 being included in ML analysis with data 0 0 0 4 record 151 is unambiguous at codon 1 record 151 is unambiguous at codon 2 record 151 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 152 ******** record read as 0 0 99 12 missing data in third codon of record 152 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 152 being included in ML analysis with data 0 0 0 12 record 152 is unambiguous at codon 1 record 152 is unambiguous at codon 2 record 152 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 153 ******** record read as 0 0 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 153 being included in ML analysis with data 0 0 0 7 record 153 is unambiguous at codon 1 record 153 is unambiguous at codon 2 record 153 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 154 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 154 being included in ML analysis with data 0 0 0 2 record 154 is unambiguous at codon 1 record 154 is unambiguous at codon 2 record 154 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 155 ******** record read as 0 0 0 3 Record 155 being included in ML analysis with data 0 0 0 3 record 155 is unambiguous at codon 1 record 155 is unambiguous at codon 2 record 155 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 156 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 156 so this record will be ignored ********* Now reading and processing record record no. 157 ******** record read as 99 99 2 3 WARNING missing data in first codon of record 157 so this record will be ignored ********* Now reading and processing record record no. 158 ******** record read as 0 0 0 8 Record 158 being included in ML analysis with data 0 0 0 8 record 158 is unambiguous at codon 1 record 158 is unambiguous at codon 2 record 158 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 159 ******** record read as 0 0 99 5 missing data in third codon of record 159 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 159 being included in ML analysis with data 0 0 0 5 record 159 is unambiguous at codon 1 record 159 is unambiguous at codon 2 record 159 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 160 ******** record read as 0 0 0 1 Record 160 being included in ML analysis with data 0 0 0 1 record 160 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 160 is unambiguous at codon 1 record 160 is unambiguous at codon 2 record 160 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 161 ******** record read as 0 0 99 4 missing data in third codon of record 161 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 161 being included in ML analysis with data 0 0 0 4 record 161 is unambiguous at codon 1 record 161 is unambiguous at codon 2 record 161 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 162 ******** record read as 0 0 0 3 Record 162 being included in ML analysis with data 0 0 0 3 record 162 is unambiguous at codon 1 record 162 is unambiguous at codon 2 record 162 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 163 ******** record read as 0 0 0 8 Record 163 being included in ML analysis with data 0 0 0 8 record 163 is unambiguous at codon 1 record 163 is unambiguous at codon 2 record 163 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 164 ******** record read as 0 0 1 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 164 being included in ML analysis with data 0 0 0 3 record 164 is unambiguous at codon 1 record 164 is unambiguous at codon 2 record 164 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 165 ******** record read as 99 0 99 1 WARNING missing data in first codon of record 165 so this record will be ignored ********* Now reading and processing record record no. 166 ******** record read as 0 0 0 2 Record 166 being included in ML analysis with data 0 0 0 2 record 166 is unambiguous at codon 1 record 166 is unambiguous at codon 2 record 166 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 167 ******** record read as 0 0 99 5 missing data in third codon of record 167 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 167 being included in ML analysis with data 0 0 0 5 record 167 is unambiguous at codon 1 record 167 is unambiguous at codon 2 record 167 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 168 ******** record read as 0 0 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 168 being included in ML analysis with data 0 0 0 2 record 168 is unambiguous at codon 1 record 168 is unambiguous at codon 2 record 168 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 169 ******** record read as 0 0 0 4 Record 169 being included in ML analysis with data 0 0 0 4 record 169 is unambiguous at codon 1 record 169 is unambiguous at codon 2 record 169 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 170 ******** record read as 0 0 0 3 Record 170 being included in ML analysis with data 0 0 0 3 record 170 is unambiguous at codon 1 record 170 is unambiguous at codon 2 record 170 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 171 ******** record read as 0 0 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 171 being included in ML analysis with data 0 0 0 1 record 171 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 171 is unambiguous at codon 1 record 171 is unambiguous at codon 2 record 171 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 172 ******** record read as 0 0 99 1 missing data in third codon of record 172 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 172 being included in ML analysis with data 0 0 0 1 record 172 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 172 is unambiguous at codon 1 record 172 is unambiguous at codon 2 record 172 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 173 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 173 so this record will be ignored ********* Now reading and processing record record no. 174 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 174 being included in ML analysis with data 0 0 0 4 record 174 is unambiguous at codon 1 record 174 is unambiguous at codon 2 record 174 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 175 ******** record read as 0 0 0 7 Record 175 being included in ML analysis with data 0 0 0 7 record 175 is unambiguous at codon 1 record 175 is unambiguous at codon 2 record 175 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 176 ******** record read as 0 0 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 176 being included in ML analysis with data 0 0 0 2 record 176 is unambiguous at codon 1 record 176 is unambiguous at codon 2 record 176 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 177 ******** record read as 0 0 0 6 Record 177 being included in ML analysis with data 0 0 0 6 record 177 is unambiguous at codon 1 record 177 is unambiguous at codon 2 record 177 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 178 ******** record read as 0 0 0 2 Record 178 being included in ML analysis with data 0 0 0 2 record 178 is unambiguous at codon 1 record 178 is unambiguous at codon 2 record 178 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 179 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 179 so this record will be ignored ********* Now reading and processing record record no. 180 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 180 being included in ML analysis with data 0 0 0 2 record 180 is unambiguous at codon 1 record 180 is unambiguous at codon 2 record 180 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 181 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 181 being included in ML analysis with data 0 0 0 2 record 181 is unambiguous at codon 1 record 181 is unambiguous at codon 2 record 181 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 182 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 182 being included in ML analysis with data 0 0 0 4 record 182 is unambiguous at codon 1 record 182 is unambiguous at codon 2 record 182 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 183 ******** record read as 0 0 0 3 Record 183 being included in ML analysis with data 0 0 0 3 record 183 is unambiguous at codon 1 record 183 is unambiguous at codon 2 record 183 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 184 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 184 being included in ML analysis with data 0 0 0 4 record 184 is unambiguous at codon 1 record 184 is unambiguous at codon 2 record 184 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 185 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 185 being included in ML analysis with data 0 0 0 4 record 185 is unambiguous at codon 1 record 185 is unambiguous at codon 2 record 185 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 186 ******** record read as 0 0 99 5 missing data in third codon of record 186 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 186 being included in ML analysis with data 0 0 0 5 record 186 is unambiguous at codon 1 record 186 is unambiguous at codon 2 record 186 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 187 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 187 being included in ML analysis with data 0 0 0 4 record 187 is unambiguous at codon 1 record 187 is unambiguous at codon 2 record 187 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 188 ******** record read as 0 0 0 8 Record 188 being included in ML analysis with data 0 0 0 8 record 188 is unambiguous at codon 1 record 188 is unambiguous at codon 2 record 188 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 189 ******** record read as 0 0 0 7 Record 189 being included in ML analysis with data 0 0 0 7 record 189 is unambiguous at codon 1 record 189 is unambiguous at codon 2 record 189 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 190 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 190 being included in ML analysis with data 0 0 0 4 record 190 is unambiguous at codon 1 record 190 is unambiguous at codon 2 record 190 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 191 ******** record read as 1 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 191 being included in ML analysis with data 1 1 0 5 record 191 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 191 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 192 ******** record read as 0 0 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 192 being included in ML analysis with data 0 0 0 8 record 192 is unambiguous at codon 1 record 192 is unambiguous at codon 2 record 192 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 193 ******** record read as 99 0 99 3 WARNING missing data in first codon of record 193 so this record will be ignored ********* Now reading and processing record record no. 194 ******** record read as 2 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 194 being included in ML analysis with data 2 0 0 3 record 194 is unambiguous at codon 1 record 194 is unambiguous at codon 2 record 194 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 195 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 195 so this record will be ignored ********* Now reading and processing record record no. 196 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 196 so this record will be ignored ********* Now reading and processing record record no. 197 ******** record read as 99 99 99 8 WARNING missing data in first codon of record 197 so this record will be ignored ********* Now reading and processing record record no. 198 ******** record read as 99 99 99 8 WARNING missing data in first codon of record 198 so this record will be ignored ********* Now reading and processing record record no. 199 ******** record read as 99 99 99 6 WARNING missing data in first codon of record 199 so this record will be ignored ********* Now reading and processing record record no. 200 ******** record read as 99 99 99 7 WARNING missing data in first codon of record 200 so this record will be ignored ********* Now reading and processing record record no. 201 ******** record read as 99 99 99 1 WARNING missing data in first codon of record 201 so this record will be ignored ********* Now reading and processing record record no. 202 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 202 being included in ML analysis with data 0 0 0 4 record 202 is unambiguous at codon 1 record 202 is unambiguous at codon 2 record 202 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 203 ******** record read as 99 0 99 2 WARNING missing data in first codon of record 203 so this record will be ignored ********* Now reading and processing record record no. 204 ******** record read as 2 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 204 being included in ML analysis with data 2 0 0 3 record 204 is unambiguous at codon 1 record 204 is unambiguous at codon 2 record 204 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 205 ******** record read as 1 2 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 205 being included in ML analysis with data 1 2 0 6 record 205 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 205 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 206 ******** record read as 0 0 0 8 Record 206 being included in ML analysis with data 0 0 0 8 record 206 is unambiguous at codon 1 record 206 is unambiguous at codon 2 record 206 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 207 ******** record read as 1 1 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 207 being included in ML analysis with data 1 1 0 8 record 207 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 207 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 208 ******** record read as 0 0 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 208 being included in ML analysis with data 0 0 0 5 record 208 is unambiguous at codon 1 record 208 is unambiguous at codon 2 record 208 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 209 ******** record read as 0 0 0 3 Record 209 being included in ML analysis with data 0 0 0 3 record 209 is unambiguous at codon 1 record 209 is unambiguous at codon 2 record 209 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 210 ******** record read as 0 1 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 210 being included in ML analysis with data 0 1 0 6 record 210 is unambiguous at codon 1 record 210 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 211 ******** record read as 1 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 211 being included in ML analysis with data 1 1 0 5 record 211 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 211 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 212 ******** record read as 0 0 0 6 Record 212 being included in ML analysis with data 0 0 0 6 record 212 is unambiguous at codon 1 record 212 is unambiguous at codon 2 record 212 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 213 ******** record read as 0 0 0 4 Record 213 being included in ML analysis with data 0 0 0 4 record 213 is unambiguous at codon 1 record 213 is unambiguous at codon 2 record 213 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 214 ******** record read as 0 0 0 5 Record 214 being included in ML analysis with data 0 0 0 5 record 214 is unambiguous at codon 1 record 214 is unambiguous at codon 2 record 214 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 215 ******** record read as 0 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 215 being included in ML analysis with data 0 2 0 3 record 215 is unambiguous at codon 1 record 215 is unambiguous at codon 2 record 215 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 216 ******** record read as 0 0 0 7 Record 216 being included in ML analysis with data 0 0 0 7 record 216 is unambiguous at codon 1 record 216 is unambiguous at codon 2 record 216 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 217 ******** record read as 99 0 2 1 WARNING missing data in first codon of record 217 so this record will be ignored ********* Now reading and processing record record no. 218 ******** record read as 0 0 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 218 being included in ML analysis with data 0 0 0 7 record 218 is unambiguous at codon 1 record 218 is unambiguous at codon 2 record 218 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 219 ******** record read as 1 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 219 being included in ML analysis with data 1 0 0 5 record 219 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 219 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 220 ******** record read as 0 0 0 4 Record 220 being included in ML analysis with data 0 0 0 4 record 220 is unambiguous at codon 1 record 220 is unambiguous at codon 2 record 220 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 221 ******** record read as 0 0 1 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 221 being included in ML analysis with data 0 0 0 7 record 221 is unambiguous at codon 1 record 221 is unambiguous at codon 2 record 221 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 222 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 222 being included in ML analysis with data 0 0 0 5 record 222 is unambiguous at codon 1 record 222 is unambiguous at codon 2 record 222 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 223 ******** record read as 0 0 0 5 Record 223 being included in ML analysis with data 0 0 0 5 record 223 is unambiguous at codon 1 record 223 is unambiguous at codon 2 record 223 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 224 ******** record read as 1 0 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 224 being included in ML analysis with data 1 0 0 7 record 224 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 224 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 225 ******** record read as 0 0 0 4 Record 225 being included in ML analysis with data 0 0 0 4 record 225 is unambiguous at codon 1 record 225 is unambiguous at codon 2 record 225 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 226 ******** record read as 2 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 226 being included in ML analysis with data 2 2 0 3 record 226 is unambiguous at codon 1 record 226 is unambiguous at codon 2 record 226 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 227 ******** record read as 0 0 99 8 missing data in third codon of record 227 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 227 being included in ML analysis with data 0 0 0 8 record 227 is unambiguous at codon 1 record 227 is unambiguous at codon 2 record 227 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 228 ******** record read as 99 0 2 5 WARNING missing data in first codon of record 228 so this record will be ignored ********* Now reading and processing record record no. 229 ******** record read as 2 0 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 229 being included in ML analysis with data 2 0 0 8 record 229 is unambiguous at codon 1 record 229 is unambiguous at codon 2 record 229 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 230 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 230 so this record will be ignored ********* Now reading and processing record record no. 231 ******** record read as 0 0 1 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 231 being included in ML analysis with data 0 0 0 8 record 231 is unambiguous at codon 1 record 231 is unambiguous at codon 2 record 231 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 232 ******** record read as 99 99 2 3 WARNING missing data in first codon of record 232 so this record will be ignored ********* Now reading and processing record record no. 233 ******** record read as 99 2 2 5 WARNING missing data in first codon of record 233 so this record will be ignored ********* Now reading and processing record record no. 234 ******** record read as 2 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 234 being included in ML analysis with data 2 2 0 3 record 234 is unambiguous at codon 1 record 234 is unambiguous at codon 2 record 234 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 235 ******** record read as 99 99 99 4 WARNING missing data in first codon of record 235 so this record will be ignored ********* Now reading and processing record record no. 236 ******** record read as 1 0 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 236 being included in ML analysis with data 1 0 0 8 record 236 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 236 is unambiguous at codon 2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 237 ******** record read as 0 0 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 237 being included in ML analysis with data 0 0 0 2 record 237 is unambiguous at codon 1 record 237 is unambiguous at codon 2 record 237 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 238 ******** record read as 0 0 0 4 Record 238 being included in ML analysis with data 0 0 0 4 record 238 is unambiguous at codon 1 record 238 is unambiguous at codon 2 record 238 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 239 ******** record read as 0 0 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 239 being included in ML analysis with data 0 0 0 8 record 239 is unambiguous at codon 1 record 239 is unambiguous at codon 2 record 239 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 240 ******** record read as 0 0 0 3 Record 240 being included in ML analysis with data 0 0 0 3 record 240 is unambiguous at codon 1 record 240 is unambiguous at codon 2 record 240 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 241 ******** record read as 99 0 0 8 WARNING missing data in first codon of record 241 so this record will be ignored ********* Now reading and processing record record no. 242 ******** record read as 99 99 99 5 WARNING missing data in first codon of record 242 so this record will be ignored ********* Now reading and processing record record no. 243 ******** record read as 0 0 0 6 Record 243 being included in ML analysis with data 0 0 0 6 record 243 is unambiguous at codon 1 record 243 is unambiguous at codon 2 record 243 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 244 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 244 being included in ML analysis with data 0 0 0 5 record 244 is unambiguous at codon 1 record 244 is unambiguous at codon 2 record 244 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 245 ******** record read as 0 0 1 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 245 being included in ML analysis with data 0 0 0 3 record 245 is unambiguous at codon 1 record 245 is unambiguous at codon 2 record 245 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 246 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 246 being included in ML analysis with data 0 0 0 5 record 246 is unambiguous at codon 1 record 246 is unambiguous at codon 2 record 246 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 247 ******** record read as 0 0 99 5 missing data in third codon of record 247 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 247 being included in ML analysis with data 0 0 0 5 record 247 is unambiguous at codon 1 record 247 is unambiguous at codon 2 record 247 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 248 ******** record read as 0 0 1 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 248 being included in ML analysis with data 0 0 0 6 record 248 is unambiguous at codon 1 record 248 is unambiguous at codon 2 record 248 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 249 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 249 being included in ML analysis with data 0 0 0 5 record 249 is unambiguous at codon 1 record 249 is unambiguous at codon 2 record 249 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 250 ******** record read as 2 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 250 being included in ML analysis with data 2 2 0 3 record 250 is unambiguous at codon 1 record 250 is unambiguous at codon 2 record 250 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 251 ******** record read as 0 0 2 4 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 251 being included in ML analysis with data 0 0 0 4 record 251 is unambiguous at codon 1 record 251 is unambiguous at codon 2 record 251 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 252 ******** record read as 0 0 0 6 Record 252 being included in ML analysis with data 0 0 0 6 record 252 is unambiguous at codon 1 record 252 is unambiguous at codon 2 record 252 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 253 ******** record read as 0 0 0 8 Record 253 being included in ML analysis with data 0 0 0 8 record 253 is unambiguous at codon 1 record 253 is unambiguous at codon 2 record 253 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 254 ******** record read as 0 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 254 being included in ML analysis with data 0 1 0 5 record 254 is unambiguous at codon 1 record 254 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 255 ******** record read as 0 0 0 5 Record 255 being included in ML analysis with data 0 0 0 5 record 255 is unambiguous at codon 1 record 255 is unambiguous at codon 2 record 255 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 256 ******** record read as 0 0 0 5 Record 256 being included in ML analysis with data 0 0 0 5 record 256 is unambiguous at codon 1 record 256 is unambiguous at codon 2 record 256 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 257 ******** record read as 0 2 2 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 257 being included in ML analysis with data 0 2 0 8 record 257 is unambiguous at codon 1 record 257 is unambiguous at codon 2 record 257 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 258 ******** record read as 0 0 0 3 Record 258 being included in ML analysis with data 0 0 0 3 record 258 is unambiguous at codon 1 record 258 is unambiguous at codon 2 record 258 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 259 ******** record read as 99 99 99 7 WARNING missing data in first codon of record 259 so this record will be ignored ********* Now reading and processing record record no. 260 ******** record read as 0 0 99 8 missing data in third codon of record 260 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 260 being included in ML analysis with data 0 0 0 8 record 260 is unambiguous at codon 1 record 260 is unambiguous at codon 2 record 260 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 261 ******** record read as 0 0 0 8 Record 261 being included in ML analysis with data 0 0 0 8 record 261 is unambiguous at codon 1 record 261 is unambiguous at codon 2 record 261 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 262 ******** record read as 0 0 0 6 Record 262 being included in ML analysis with data 0 0 0 6 record 262 is unambiguous at codon 1 record 262 is unambiguous at codon 2 record 262 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 263 ******** record read as 0 0 0 8 Record 263 being included in ML analysis with data 0 0 0 8 record 263 is unambiguous at codon 1 record 263 is unambiguous at codon 2 record 263 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 264 ******** record read as 0 0 0 4 Record 264 being included in ML analysis with data 0 0 0 4 record 264 is unambiguous at codon 1 record 264 is unambiguous at codon 2 record 264 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 265 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 265 being included in ML analysis with data 0 0 0 3 record 265 is unambiguous at codon 1 record 265 is unambiguous at codon 2 record 265 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 266 ******** record read as 0 0 0 8 Record 266 being included in ML analysis with data 0 0 0 8 record 266 is unambiguous at codon 1 record 266 is unambiguous at codon 2 record 266 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 267 ******** record read as 0 0 0 7 Record 267 being included in ML analysis with data 0 0 0 7 record 267 is unambiguous at codon 1 record 267 is unambiguous at codon 2 record 267 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 268 ******** record read as 0 0 0 6 Record 268 being included in ML analysis with data 0 0 0 6 record 268 is unambiguous at codon 1 record 268 is unambiguous at codon 2 record 268 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 269 ******** record read as 0 0 0 8 Record 269 being included in ML analysis with data 0 0 0 8 record 269 is unambiguous at codon 1 record 269 is unambiguous at codon 2 record 269 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 270 ******** record read as 0 0 0 4 Record 270 being included in ML analysis with data 0 0 0 4 record 270 is unambiguous at codon 1 record 270 is unambiguous at codon 2 record 270 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 271 ******** record read as 2 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 271 being included in ML analysis with data 2 2 0 3 record 271 is unambiguous at codon 1 record 271 is unambiguous at codon 2 record 271 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 272 ******** record read as 0 0 0 3 Record 272 being included in ML analysis with data 0 0 0 3 record 272 is unambiguous at codon 1 record 272 is unambiguous at codon 2 record 272 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 273 ******** record read as 0 0 0 2 Record 273 being included in ML analysis with data 0 0 0 2 record 273 is unambiguous at codon 1 record 273 is unambiguous at codon 2 record 273 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 274 ******** record read as 1 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 274 being included in ML analysis with data 1 1 0 5 record 274 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 274 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 275 ******** record read as 2 0 99 5 missing data in third codon of record 275 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 275 being included in ML analysis with data 2 0 0 5 record 275 is unambiguous at codon 1 record 275 is unambiguous at codon 2 record 275 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 276 ******** record read as 99 99 99 2 WARNING missing data in first codon of record 276 so this record will be ignored ********* Now reading and processing record record no. 277 ******** record read as 0 0 0 8 Record 277 being included in ML analysis with data 0 0 0 8 record 277 is unambiguous at codon 1 record 277 is unambiguous at codon 2 record 277 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 278 ******** record read as 0 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 278 being included in ML analysis with data 0 2 0 2 record 278 is unambiguous at codon 1 record 278 is unambiguous at codon 2 record 278 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 279 ******** record read as 0 0 0 5 Record 279 being included in ML analysis with data 0 0 0 5 record 279 is unambiguous at codon 1 record 279 is unambiguous at codon 2 record 279 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 280 ******** record read as 0 0 0 5 Record 280 being included in ML analysis with data 0 0 0 5 record 280 is unambiguous at codon 1 record 280 is unambiguous at codon 2 record 280 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 281 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 281 being included in ML analysis with data 0 0 0 2 record 281 is unambiguous at codon 1 record 281 is unambiguous at codon 2 record 281 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 282 ******** record read as 1 1 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 282 being included in ML analysis with data 1 1 0 3 record 282 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 282 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 283 ******** record read as 0 0 1 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 283 being included in ML analysis with data 0 0 0 3 record 283 is unambiguous at codon 1 record 283 is unambiguous at codon 2 record 283 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 284 ******** record read as 0 0 0 8 Record 284 being included in ML analysis with data 0 0 0 8 record 284 is unambiguous at codon 1 record 284 is unambiguous at codon 2 record 284 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 285 ******** record read as 0 0 0 4 Record 285 being included in ML analysis with data 0 0 0 4 record 285 is unambiguous at codon 1 record 285 is unambiguous at codon 2 record 285 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 286 ******** record read as 0 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 286 being included in ML analysis with data 0 1 0 5 record 286 is unambiguous at codon 1 record 286 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 287 ******** record read as 0 0 99 3 missing data in third codon of record 287 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 287 being included in ML analysis with data 0 0 0 3 record 287 is unambiguous at codon 1 record 287 is unambiguous at codon 2 record 287 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 288 ******** record read as 0 0 0 4 Record 288 being included in ML analysis with data 0 0 0 4 record 288 is unambiguous at codon 1 record 288 is unambiguous at codon 2 record 288 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 289 ******** record read as 0 1 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 289 being included in ML analysis with data 0 1 0 7 record 289 is unambiguous at codon 1 record 289 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 290 ******** record read as 0 0 0 2 Record 290 being included in ML analysis with data 0 0 0 2 record 290 is unambiguous at codon 1 record 290 is unambiguous at codon 2 record 290 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 291 ******** record read as 0 0 1 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 291 being included in ML analysis with data 0 0 0 7 record 291 is unambiguous at codon 1 record 291 is unambiguous at codon 2 record 291 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 292 ******** record read as 99 0 99 7 WARNING missing data in first codon of record 292 so this record will be ignored ********* Now reading and processing record record no. 293 ******** record read as 0 1 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 293 being included in ML analysis with data 0 1 0 5 record 293 is unambiguous at codon 1 record 293 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 294 ******** record read as 0 0 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 294 being included in ML analysis with data 0 0 0 6 record 294 is unambiguous at codon 1 record 294 is unambiguous at codon 2 record 294 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 295 ******** record read as 0 1 99 4 missing data in third codon of record 295 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 295 being included in ML analysis with data 0 1 0 4 record 295 is unambiguous at codon 1 record 295 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 296 ******** record read as 0 0 99 2 missing data in third codon of record 296 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 296 being included in ML analysis with data 0 0 0 2 record 296 is unambiguous at codon 1 record 296 is unambiguous at codon 2 record 296 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 297 ******** record read as 0 1 1 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 297 being included in ML analysis with data 0 1 0 3 record 297 is unambiguous at codon 1 record 297 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 298 ******** record read as 0 0 99 7 missing data in third codon of record 298 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 298 being included in ML analysis with data 0 0 0 7 record 298 is unambiguous at codon 1 record 298 is unambiguous at codon 2 record 298 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 299 ******** record read as 1 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 299 being included in ML analysis with data 1 2 0 2 record 299 is unambiguous at codon 1 record 299 is unambiguous at codon 2 record 299 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 300 ******** record read as 0 0 0 5 Record 300 being included in ML analysis with data 0 0 0 5 record 300 is unambiguous at codon 1 record 300 is unambiguous at codon 2 record 300 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 301 ******** record read as 0 0 0 4 Record 301 being included in ML analysis with data 0 0 0 4 record 301 is unambiguous at codon 1 record 301 is unambiguous at codon 2 record 301 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 302 ******** record read as 0 0 0 2 Record 302 being included in ML analysis with data 0 0 0 2 record 302 is unambiguous at codon 1 record 302 is unambiguous at codon 2 record 302 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 303 ******** record read as 0 0 0 4 Record 303 being included in ML analysis with data 0 0 0 4 record 303 is unambiguous at codon 1 record 303 is unambiguous at codon 2 record 303 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 304 ******** record read as 0 0 0 4 Record 304 being included in ML analysis with data 0 0 0 4 record 304 is unambiguous at codon 1 record 304 is unambiguous at codon 2 record 304 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 305 ******** record read as 0 0 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 305 being included in ML analysis with data 0 0 0 5 record 305 is unambiguous at codon 1 record 305 is unambiguous at codon 2 record 305 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 306 ******** record read as 0 0 0 6 Record 306 being included in ML analysis with data 0 0 0 6 record 306 is unambiguous at codon 1 record 306 is unambiguous at codon 2 record 306 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 307 ******** record read as 0 0 0 2 Record 307 being included in ML analysis with data 0 0 0 2 record 307 is unambiguous at codon 1 record 307 is unambiguous at codon 2 record 307 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 308 ******** record read as 0 0 0 4 Record 308 being included in ML analysis with data 0 0 0 4 record 308 is unambiguous at codon 1 record 308 is unambiguous at codon 2 record 308 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 309 ******** record read as 0 1 1 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 309 being included in ML analysis with data 0 1 0 2 record 309 is unambiguous at codon 1 record 309 is unambiguous at codon 2 record 309 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 310 ******** record read as 0 0 0 2 Record 310 being included in ML analysis with data 0 0 0 2 record 310 is unambiguous at codon 1 record 310 is unambiguous at codon 2 record 310 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 311 ******** record read as 0 0 0 2 Record 311 being included in ML analysis with data 0 0 0 2 record 311 is unambiguous at codon 1 record 311 is unambiguous at codon 2 record 311 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 312 ******** record read as 1 1 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 312 being included in ML analysis with data 1 1 0 3 record 312 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 312 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 313 ******** record read as 0 0 0 5 Record 313 being included in ML analysis with data 0 0 0 5 record 313 is unambiguous at codon 1 record 313 is unambiguous at codon 2 record 313 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 314 ******** record read as 0 0 0 2 Record 314 being included in ML analysis with data 0 0 0 2 record 314 is unambiguous at codon 1 record 314 is unambiguous at codon 2 record 314 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 315 ******** record read as 0 0 0 2 Record 315 being included in ML analysis with data 0 0 0 2 record 315 is unambiguous at codon 1 record 315 is unambiguous at codon 2 record 315 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 316 ******** record read as 0 2 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 316 being included in ML analysis with data 0 2 0 5 record 316 is unambiguous at codon 1 record 316 is unambiguous at codon 2 record 316 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 317 ******** record read as 1 1 1 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 317 being included in ML analysis with data 1 1 0 5 record 317 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 317 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 318 ******** record read as 0 0 0 2 Record 318 being included in ML analysis with data 0 0 0 2 record 318 is unambiguous at codon 1 record 318 is unambiguous at codon 2 record 318 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 319 ******** record read as 0 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 319 being included in ML analysis with data 0 2 0 2 record 319 is unambiguous at codon 1 record 319 is unambiguous at codon 2 record 319 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 320 ******** record read as 0 0 0 2 Record 320 being included in ML analysis with data 0 0 0 2 record 320 is unambiguous at codon 1 record 320 is unambiguous at codon 2 record 320 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 321 ******** record read as 0 0 0 2 Record 321 being included in ML analysis with data 0 0 0 2 record 321 is unambiguous at codon 1 record 321 is unambiguous at codon 2 record 321 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 322 ******** record read as 0 1 2 7 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 322 being included in ML analysis with data 0 1 0 7 record 322 is unambiguous at codon 1 record 322 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 323 ******** record read as 0 0 0 2 Record 323 being included in ML analysis with data 0 0 0 2 record 323 is unambiguous at codon 1 record 323 is unambiguous at codon 2 record 323 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 324 ******** record read as 0 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 324 being included in ML analysis with data 0 1 0 5 record 324 is unambiguous at codon 1 record 324 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 325 ******** record read as 0 0 0 8 Record 325 being included in ML analysis with data 0 0 0 8 record 325 is unambiguous at codon 1 record 325 is unambiguous at codon 2 record 325 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 326 ******** record read as 0 0 1 8 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 326 being included in ML analysis with data 0 0 0 8 record 326 is unambiguous at codon 1 record 326 is unambiguous at codon 2 record 326 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 327 ******** record read as 2 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 327 being included in ML analysis with data 2 0 0 2 record 327 is unambiguous at codon 1 record 327 is unambiguous at codon 2 record 327 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 328 ******** record read as 1 1 2 6 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 328 being included in ML analysis with data 1 1 0 6 record 328 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 328 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 329 ******** record read as 0 2 2 1 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 329 being included in ML analysis with data 0 2 0 1 record 329 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 329 is unambiguous at codon 1 record 329 is unambiguous at codon 2 record 329 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 330 ******** record read as 0 1 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 330 being included in ML analysis with data 0 1 0 2 record 330 is unambiguous at codon 1 record 330 is unambiguous at codon 2 record 330 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 331 ******** record read as 0 0 0 2 Record 331 being included in ML analysis with data 0 0 0 2 record 331 is unambiguous at codon 1 record 331 is unambiguous at codon 2 record 331 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 332 ******** record read as 0 0 0 2 Record 332 being included in ML analysis with data 0 0 0 2 record 332 is unambiguous at codon 1 record 332 is unambiguous at codon 2 record 332 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 333 ******** record read as 0 0 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 333 being included in ML analysis with data 0 0 0 2 record 333 is unambiguous at codon 1 record 333 is unambiguous at codon 2 record 333 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 334 ******** record read as 0 0 0 6 Record 334 being included in ML analysis with data 0 0 0 6 record 334 is unambiguous at codon 1 record 334 is unambiguous at codon 2 record 334 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 335 ******** record read as 0 0 0 4 Record 335 being included in ML analysis with data 0 0 0 4 record 335 is unambiguous at codon 1 record 335 is unambiguous at codon 2 record 335 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 336 ******** record read as 1 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 336 being included in ML analysis with data 1 1 0 5 record 336 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 336 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 337 ******** record read as 0 0 0 5 Record 337 being included in ML analysis with data 0 0 0 5 record 337 is unambiguous at codon 1 record 337 is unambiguous at codon 2 record 337 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 338 ******** record read as 2 2 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 338 being included in ML analysis with data 2 2 0 3 record 338 is unambiguous at codon 1 record 338 is unambiguous at codon 2 record 338 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 339 ******** record read as 2 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 339 being included in ML analysis with data 2 2 0 2 record 339 is unambiguous at codon 1 record 339 is unambiguous at codon 2 record 339 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 340 ******** record read as 0 0 0 2 Record 340 being included in ML analysis with data 0 0 0 2 record 340 is unambiguous at codon 1 record 340 is unambiguous at codon 2 record 340 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 341 ******** record read as 0 0 0 2 Record 341 being included in ML analysis with data 0 0 0 2 record 341 is unambiguous at codon 1 record 341 is unambiguous at codon 2 record 341 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 342 ******** record read as 0 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 342 being included in ML analysis with data 0 2 0 2 record 342 is unambiguous at codon 1 record 342 is unambiguous at codon 2 record 342 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 343 ******** record read as 0 0 0 1 Record 343 being included in ML analysis with data 0 0 0 1 record 343 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 343 is unambiguous at codon 1 record 343 is unambiguous at codon 2 record 343 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 344 ******** record read as 0 0 99 2 missing data in third codon of record 344 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 344 being included in ML analysis with data 0 0 0 2 record 344 is unambiguous at codon 1 record 344 is unambiguous at codon 2 record 344 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 345 ******** record read as 1 1 2 5 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 345 being included in ML analysis with data 1 1 0 5 record 345 is ambiguous.... codon 1 is heterozygous and has MOI>2 record 345 is ambiguous.... codon 2 is heterozygous and has MOI>2 Cannot determine the 2-codon haplotypes because of ambiguity in one or more of the constituent codons ********* Now reading and processing record record no. 346 ******** record read as 0 0 0 2 Record 346 being included in ML analysis with data 0 0 0 2 record 346 is unambiguous at codon 1 record 346 is unambiguous at codon 2 record 346 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 347 ******** record read as 0 2 2 2 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 347 being included in ML analysis with data 0 2 0 2 record 347 is unambiguous at codon 1 record 347 is unambiguous at codon 2 record 347 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 348 ******** record read as 0 0 99 2 missing data in third codon of record 348 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 348 being included in ML analysis with data 0 0 0 2 record 348 is unambiguous at codon 1 record 348 is unambiguous at codon 2 record 348 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 349 ******** record read as 0 0 0 1 Record 349 being included in ML analysis with data 0 0 0 1 record 349 has MOI=1 so can be incorporated in the analysis directly counting SNPs and haplotyes in samples with MOI=1 record 349 is unambiguous at codon 1 record 349 is unambiguous at codon 2 record 349 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 350 ******** record read as 0 0 0 2 Record 350 being included in ML analysis with data 0 0 0 2 record 350 is unambiguous at codon 1 record 350 is unambiguous at codon 2 record 350 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 351 ******** record read as 0 0 2 3 User has instructed programme to only investigate two codons, other must be set to wildtype i.e. have values 0 programe will automatically recode and read genotypes at other codons as wildtype Record 351 being included in ML analysis with data 0 0 0 3 record 351 is unambiguous at codon 1 record 351 is unambiguous at codon 2 record 351 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 352 ******** record read as 0 0 99 4 missing data in third codon of record 352 this data is not required because this codon is not being analysed Record will be included in analysis with missing data being set to 0 i.e. homozygous wildtype Record 352 being included in ML analysis with data 0 0 0 4 record 352 is unambiguous at codon 1 record 352 is unambiguous at codon 2 record 352 is unambiguous at haplotypes defined by codon 1 and 2 ********* Now reading and processing record record no. 353 ******** last line is i1=0 i2=0 i3=0 i4=4 total no.of observations incorporated into Maximum likleihood analysis=298 total number of clones incorporated into Maximum likleihood analysis=1220 finished reading datafile ************************************************************************* Frequency estimates obtained by direct counting of codons and haplotypes in samples with MOI=1 Note that CI are obtained by ML so may be too narrow if mutation frequency close to 0 or 100 percent. See User Manual section _What’s new in Version 2.1.1_ note 2 for details and solution. Codon 1....there were 2 mutants from a total of 17 so estimated frequency is 0.117647 with 95% CI 0.018647 -> 0.326647 Codon 2...there were 3 mutants from a total of 17 so estimated frequency is 0.176471 with 95% CI 0.045471 -> 0.401471 There were 14 haplotypes of type [0][0] from a total of 17 so estimated frequency is 0.823529 with 95% CI 0.598529 -> 0.954529 There were 1 haplotypes of type [0][1] from a total of 17 so estimated frequency is 0.058824 with 95% CI 0.002824 -> 0.239824 There were 0 haplotypes of type [1][0] from a total of 17 so estimated frequency is 0.000000 with 95% CI 0.000000 -> 0.111000 There were 2 haplotypes of type [1][1] from a total of 17 so estimated frequency is 0.117647 with 95% CI 0.018647 -> 0.326647 ************************************************************************* SNP Frequency estimates obtained by direct counting in samples with MOI<=2 Note that CI are obtained by ML so may be too narrow if mutation frequency close to 0 or 100 percent. See User Manual section _What’s new in Version 2.1.1_ note 2 for details and solution. Codon 1...there were 14 mutants from a total of 149 so estimated frequency is 0.093960 with 95% CI 0.052960 -> 0.148960 Codon 2...there were 23 mutants from a total of 149 so estimated frequency is 0.154362 with 95% CI 0.101362 -> 0.220362 ************************************************************************* Frequency estimates obtained by direct counting of codons and haplotypes in unambiguous samples Note that CI are obtained by ML so may be too narrow if mutation frequency close to 0 or 100 percent. See User Manual section _What’s new in Version 2.1.1_ note 2 for details and solution. Codon 1....there were 48 mutants from a total of 1131 so estimated frequency is 0.042440 with 95% CI 0.031440 -> 0.056440 Codon 2...there were 77 mutants from a total of 1108 so estimated frequency is 0.069495 with 95% CI 0.054495 -> 0.086495 There were 977 haplotypes of type [0][0] from a total of 1071 so estimated frequency is 0.912232 with 95% CI 0.893232 -> 0.929232 There were 47 haplotypes of type [0][1] from a total of 1071 so estimated frequency is 0.043884 with 95% CI 0.031884 -> 0.057884 There were 24 haplotypes of type [1][0] from a total of 1071 so estimated frequency is 0.022409 with 95% CI 0.014409 -> 0.033409 There were 23 haplotypes of type [1][1] from a total of 1071 so estimated frequency is 0.021475 with 95% CI 0.013475 -> 0.032475 ********************************************************* Estimates of prevalence Note that joint prevalences are simply blood sample that contain that combination of markers It does not mean that the markers are in the same parasites I'm not a fan of prevalences and definitely view joint prevalences with deep suspicion However I realise opinions differ so report them here I haven't fully tested these calculations. They are simple but bugs creep into programmes really easily HENCE DO NOT RELY ON THEM!!! always double check e.g. by direct counting and let me know if you find errors prevalence of wildtype at position 1 is 283 out of 299 samples prevalence of mutations at position 1 is 35 out of 299 samples prevalence of wildtype at position 2 is 293 out of 318 samples prevalence of mutations at position 2 is 54 out of 318 samples joint prevalence of mutations at positions 1 and 2 where '-' is absence of marker an '+' is presence combination [-][-]is 268 out of 298 samples combination [+][-]is 24 out of 298 samples combination [-][+]is 42 out of 298 samples combination [+][+]is 24 out of 298 samples ************************************************************************* About to initiate ML analysis starting precision level 2, current best estimate of max LL is -304.271327 starting precision level 3, current best estimate of max LL is -286.147951 starting precision level 4, current best estimate of max LL is -285.229549 starting precision level 5, current best estimate of max LL is -285.225915 starting precision level 6, current best estimate of max LL is -285.225908 starting precision level 7, current best estimate of max LL is -285.225908 starting precision level 8, current best estimate of max LL is -285.225908 best ML estimates have been found total no. of records in field data set=298 maximum log likelihood=-285.2259076444011600000 nat log of the multinomial coefficient is 200.804230 This contains a constant, the multinomial coefficient, whose log value is 200.804230 so maximum log likelihood excluding multinomial coefficient=-486.0301379141886900000 best estimate of freq[0][0][0]=0.888392 best estimate of freq[0][0][1]=0.000000 best estimate of freq[0][1][0]=0.055702 best estimate of freq[0][1][1]=0.000000 best estimate of freq[1][0][0]=0.026199 best estimate of freq[1][0][1]=0.000000 best estimate of freq[1][1][0]=0.029707 best estimate of freq[1][1][1]=0.000000 searching for CI for allele[0][0][0] current best estimate for freq is 0.888392 lower CI for allele[0][0][0] does not include zero find_CI has found lower CI for allele[0][0][0]=0.868438 find_CI has found upper CI for allele[0][0][0]=0.906703 NOT searching for CI for invariant allele[0][0][1] searching for CI for allele[0][1][0] current best estimate for freq is 0.055702 lower CI for allele[0][1][0] does not include zero find_CI has found lower CI for allele[0][1][0]=0.042647 find_CI has found upper CI for allele[0][1][0]=0.071379 NOT searching for CI for invariant allele[0][1][1] searching for CI for allele[1][0][0] current best estimate for freq is 0.026199 lower CI for allele[1][0][0] does not include zero find_CI has found lower CI for allele[1][0][0]=0.017193 find_CI has found upper CI for allele[1][0][0]=0.037611 NOT searching for CI for invariant allele[1][0][1] searching for CI for allele[1][1][0] current best estimate for freq is 0.029707 lower CI for allele[1][1][0] does not include zero find_CI has found lower CI for allele[1][1][0]=0.020423 find_CI has found upper CI for allele[1][1][0]=0.041077 NOT searching for CI for invariant allele[1][1][1] Best estimates with 95 percent CI for allele frequencies are as follows allele[0][0][0] 0.888392 CI 0.868438 to 0.906703 allele[0][0][1] 0.000000 CI 0.000000 to 0.000000 allele[0][1][0] 0.055702 CI 0.042647 to 0.071379 allele[0][1][1] 0.000000 CI 0.000000 to 0.000000 allele[1][0][0] 0.026199 CI 0.017193 to 0.037611 allele[1][0][1] 0.000000 CI 0.000000 to 0.000000 allele[1][1][0] 0.029707 CI 0.020423 to 0.041077 allele[1][1][1] 0.000000 CI 0.000000 to 0.000000