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MEGA2 4.7.0
Copyright (C) 1999-2014 Robert Baron, Charles P. Kollar,
Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill,
Daniel E. Weeks, and University of Pittsburgh
Last updated: Jul 22 2014, 12:55:24 , valid until June 15, 2015.
Compiled with gcc version 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)
Mega2 comes with ABSOLUTELY NO WARRANTY.
See LICENSE.txt for terms of copying, modifying & redistributing Mega2.
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NOTE: If you have previously used explicit numbers for sex chromosomes, BEWARE!
We have changed the numbers to be compatible with PLINK. 23 still codes for X,
but 24 codes for Y and 25 Codes for XY.
Running Mega2 in batch mode from MEGA2.BATCH.pre
Input filenames and missing value indicator read in from batch file.
Analysis option read in from batch file.
Markers, chromosome(s) and read in from batch file.
Trait selection(s) read in from batch file.
Keyword Input_PLINK_Map_File not in batch file, PLINK map file assumed to be unspecified.
Keyword Input_Omit_File not in batch file, Omit file assumed to be unspecified.
Keyword Input_Frequency_File not in batch file, Frequency file assumed to be unspecified.
Keyword Input_Penetrance_File not in batch file, Penetrance file assumed to be unspecified.
Keyword Input_Aux_File not in batch file, Aux file assumed to be unspecified.
Keyword Input_Phenotype_File not in batch file, Phenotype file assumed to be unspecified.
Keyword Input_Path not in batch file, using default '.' (current directory).
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Mega2 version 4.7.0
Run date: 2014-7-22-13-08
This file created on Tue Jul 22 13:08:32 2014
Input file names
# Pedigree file: pedin.pre.05
# Locus file: datain.05
# Map file: map.05
Untyped pedigree option: Include all pedigrees whether typed or not
Mendelianly-inconsistent genotypes included in output.
Half-typed individuals' genotypes included in output.
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Analysis option: Mendel7+.
Input Format: Linkage format
Pedigree, names and map file specified as LINKAGE format.
Input files will be read in as LINKAGE format files.
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Checking format of pedigree file pedin.pre.05.
Pedigree file pedin.pre.05 is in pre-makeped format.
Locus file is in Linkage format
Reading in map file map.05.
Data read in from map file.
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Locus file is in LINKAGE format.
Total number of loci = 5
2 trait loci
1 Affection status locus:
TRAIT
1 Quantitative locus:
Q1
3 Marker loci
Number of loci found per chromosome (chromosome:number)
5:3
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Data read in from pedigree file:
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Input pedigree data contains:
Input pedigree file is in pre-makeped format.
Marker Genotypes
Fully Half
Pedigrees People Males Females Typed Typed Total
TOTAL 2 21 9 12 63 0 63
Typed 2 21 9 12
Untyped 0 0 0 0
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Pedigree exclusion option : Include all pedigrees whether typed or not.
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After excluding untyped pedigrees :
Input pedigree file is in pre-makeped format.
Marker Genotypes
Fully Half
Pedigrees People Males Females Typed Typed Total
TOTAL 2 21 9 12 63 0 63
Typed 2 21 9 12
Untyped 0 0 0 0
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Selected map Map.
Selected chromosome 5
Output will combine markers and the following selected traits:
TRAIT [MARKERS]
After selecting traits and covariates
1 trait locus
1 Affection status locus:
TRAIT
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Pedigree statistics after selecting chromosomes and marker loci:
Marker Genotypes
Fully Half
Pedigrees People Males Females Typed Typed Total
TOTAL 2 21 9 12 63 0 63
Typed 2 21 9 12
Untyped 0 0 0 0
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Person id in output pedigree file = Individual id
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Pedigree id in output pedigree file = Premakeped pedigree number.
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Mega2 created the following file(s) for Mendel7+:
Definition file: mendel_locus.05
Pedigree file: mendel_ped.05
Map file: mendel_map.05
Control file: mendel_control.05
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Output is in ../example_output_pre
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If you use Mega2 as part of a published work, please reference
Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2005)
Mega2: data-handling for facilitating genetic linkage and association analyses.
Bioinformatics. 2005 May 15;21(10):2556-7, PMID: 15746282
as well as the version used, which is currently Version 4.7.0
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See run summaries in current directory .
MEGA2.LOG, MEGA2.ERR, MEGA2.KEYS