(Click any preview image to download a full sized PDF version)

Click here to download the Marker QC Detail report file (1.4 KB) tab delimited
Click here to download the Subject QC Detail report file (1.4 KB) tab delimited
	All tinywga QC Plots joined into a single pdf
	All tinywga QC Plots 3 by 3 to a page
	Marker HWE	Worst data
	Ranked Marker HWE
	LogQQ plot Marker HWE
	Marker Missing Genotype	Worst data
	Ranked Marker Missing Genotype
	Marker MAF	Worst data
	Ranked Marker MAF
	Subject Missing Genotype	Worst data
	Ranked Subject Missing Genotype
	Subject F Statistic
	Ranked Subject F Statistic
	F Statistic Subject F Statistic

---

All output files from the QC run are available below

FQNormtinywga_s_het_cum.jpg (30.2 KB)

FQNormtinywga_s_het_cum.pdf (7.1 KB)

MarkerDetails_rgQCtest1.xls (1.4 KB)

QQtinywga_logphweunaff_cum.jpg (33.0 KB)

QQtinywga_logphweunaff_cum.pdf (6.6 KB)

Ranked_Marker_HWE.xls (763 B)

Ranked_Marker_MAF.xls (564 B)

Ranked_Marker_Missing_Genotype.xls (659 B)

Ranked_Subject_Missing_Genotype.xls (804 B)

SubjectDetails_rgQCtest1.xls (1.4 KB)

ldp_tinywga.bed (143 B)

ldp_tinywga.bim (392 B)

ldp_tinywga.fam (603 B)

ldp_tinywga.log (2.0 KB)

tinywga.fmendel (378 B)

tinywga.frq (1.2 KB)

tinywga.het (2.5 KB)

tinywga.hwe (6.5 KB)

tinywga.imendel (612 B)

tinywga.imiss (1.9 KB)

tinywga.lmendel (571 B)

tinywga.lmiss (1.1 KB)

tinywga.log (1.9 KB)

tinywga.mendel (56 B)

tinywga.prune.in (140 B)

tinywga.prune.out (110 B)

tinywga.sexcheck (2.5 KB)

tinywga_All_3x3-0.jpg (45.2 KB)

tinywga_All_3x3-1.jpg (19.3 KB)

tinywga_All_3x3.pdf (82.4 KB)

tinywga_All_Paged-0.jpg (13.6 KB)

tinywga_All_Paged-1.jpg (26.3 KB)

tinywga_All_Paged-10.jpg (31.4 KB)

tinywga_All_Paged-11.jpg (29.8 KB)

tinywga_All_Paged-2.jpg (32.3 KB)

tinywga_All_Paged-3.jpg (11.1 KB)

tinywga_All_Paged-4.jpg (26.7 KB)

tinywga_All_Paged-5.jpg (18.4 KB)

tinywga_All_Paged-6.jpg (28.1 KB)

tinywga_All_Paged-7.jpg (11.9 KB)

tinywga_All_Paged-8.jpg (29.6 KB)

tinywga_All_Paged-9.jpg (17.9 KB)

tinywga_All_Paged.pdf (81.9 KB)

tinywga_fracmiss.jpg (12.0 KB)

tinywga_fracmiss.pdf (6.4 KB)

tinywga_fracmiss_cum.jpg (30.0 KB)

tinywga_fracmiss_cum.pdf (7.0 KB)

tinywga_logphweunaff.jpg (13.6 KB)

tinywga_logphweunaff.pdf (5.7 KB)

tinywga_logphweunaff_cum.jpg (26.8 KB)

tinywga_logphweunaff_cum.pdf (5.8 KB)

tinywga_maf.jpg (18.5 KB)

tinywga_maf.pdf (6.4 KB)

tinywga_maf_cum.jpg (28.5 KB)

tinywga_maf_cum.pdf (6.0 KB)

tinywga_missfrac.jpg (11.1 KB)

tinywga_missfrac.pdf (5.9 KB)

tinywga_missfrac_cum.jpg (27.3 KB)

tinywga_missfrac_cum.pdf (5.9 KB)

tinywga_s_het.jpg (18.0 KB)

tinywga_s_het.pdf (6.8 KB)

tinywga_s_het_cum.jpg (31.9 KB)

tinywga_s_het_cum.pdf (7.3 KB)

QC run log contents

## subject reports starting at 19/05/2010 15:15:38
## imissfile /opt/galaxy/test-data/rgtestouts/rgQC/tinywga.imiss contained 40 ids
### writing /opt/galaxy/test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls report with ['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat']## marker reports starting at 19/05/2010 15:15:38
hwe header testpos=2,ppos=8,snppos=1
## starting plotpage, newfpath=/opt/galaxy/test-data/rgtestouts/rgQC,m=[['snp', 'chromosome', 'offset', 'maf', 'a1', 'a2', 'missfrac', 'p_hwe_all', 'logp_hwe_all', 'p_hwe_unaff', 'logp_hwe_unaff', 'N_Mendel'], ['rs2283802', '22', '21784722', '0.2593', '4', '2', '0', '0.638', '0.195179', '0.638', '0.195179', '0']],s=[['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat'], ['101', '1', '0.04', '0', '2', '0', 'PROBLEM', 'nan', '-0.03355']]/n## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner

@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
	--noweb
	--out tinywga
	--bfile /opt/galaxy/test-data/tinywga
	--mind 1.0
	--geno 1.0
	--maf 0.0
	--freq

Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
Writing allele frequencies (founders-only) to [ tinywga.frq ] 

Analysis finished: Wed May 19 15:15:38 2010


@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
	--noweb
	--out tinywga
	--bfile /opt/galaxy/test-data/tinywga
	--mind 1.0
	--geno 1.0
	--maf 0.0
	--hwe 0.0
	--missing
	--hardy

Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
Writing Hardy-Weinberg tests (founders-only) to [ tinywga.hwe ] 
0 markers to be excluded based on HWE test ( p <= 0 )
	0 markers failed HWE test in cases
	0 markers failed HWE test in controls
Writing individual missingness information to [ tinywga.imiss ] 
Writing locus missingness information to [ tinywga.lmiss ] 
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex

Analysis finished: Wed May 19 15:15:38 2010


@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
	--noweb
	--out tinywga
	--bfile /opt/galaxy/test-data/tinywga
	--mind 1.0
	--geno 1.0
	--maf 0.0
	--mendel

Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
14 nuclear families, 1 founder singletons found
13 non-founders with 2 parents in 13 nuclear families
0 non-founders without 2 parents in 0 nuclear families
10 affected offspring trios
0 phenotypically discordant parent pairs found
Converting data to Individual-major format
Writing all Mendel errors to [ tinywga.mendel ]
Writing per-offspring Mendel summary to [ tinywga.imendel ]
Writing per-family Mendel summary to [ tinywga.fmendel ]
Writing per-locus Mendel summary to [ tinywga.lmendel ]
0 Mendel errors detected in total

Analysis finished: Wed May 19 15:15:38 2010


@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
	--noweb
	--out tinywga
	--bfile /opt/galaxy/test-data/tinywga
	--mind 1.0
	--geno 1.0
	--maf 0.0
	--check-sex

Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
Converting data to Individual-major format
Writing X-chromosome sex check results to [ tinywga.sexcheck ] 

Analysis finished: Wed May 19 15:15:38 2010

## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner



@----------------------------------------------------------@

|        PLINK!       |     v1.06      |   24/Apr/2009     |

|----------------------------------------------------------|

|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |

|----------------------------------------------------------|

|  For documentation, citation & bug-report instructions:  |

|        http://pngu.mgh.harvard.edu/purcell/plink/        |

@----------------------------------------------------------@



Skipping web check... [ --noweb ] 

Writing this text to log file [ tinywga.log ]

Analysis started: Wed May 19 15:15:38 2010



Options in effect:

	--noweb

	--bfile /opt/galaxy/test-data/tinywga

	--indep-pairwise 40 20 0.5

	--out tinywga



Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 

25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]

Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 

40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 

40 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

10 cases, 30 controls and 0 missing

21 males, 19 females, and 0 of unspecified sex

Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 

Detected that binary PED file is v1.00 SNP-major mode

Before frequency and genotyping pruning, there are 25 SNPs

27 founders and 13 non-founders found

Total genotyping rate in remaining individuals is 0.995

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 25 SNPs

After filtering, 10 cases, 30 controls and 0 missing

After filtering, 21 males, 19 females, and 0 of unspecified sex

Performing LD-based pruning...

Writing pruned-in SNPs to [ tinywga.prune.in ]

Writing pruned-out SNPs to [ tinywga.prune.out ]

Scanning from chromosome 22 to 22



Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]

For chromosome 22, 11 SNPs pruned out, 14 remaining



Analysis finished: Wed May 19 15:15:38 2010







@----------------------------------------------------------@

|        PLINK!       |     v1.06      |   24/Apr/2009     |

|----------------------------------------------------------|

|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |

|----------------------------------------------------------|

|  For documentation, citation & bug-report instructions:  |

|        http://pngu.mgh.harvard.edu/purcell/plink/        |

@----------------------------------------------------------@



Skipping web check... [ --noweb ] 

Writing this text to log file [ ldp_tinywga.log ]

Analysis started: Wed May 19 15:15:38 2010



Options in effect:

	--noweb

	--bfile /opt/galaxy/test-data/tinywga

	--extract tinywga.prune.in

	--make-bed

	--out ldp_tinywga



Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 

25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]

Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 

40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 

40 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

10 cases, 30 controls and 0 missing

21 males, 19 females, and 0 of unspecified sex

Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 

Detected that binary PED file is v1.00 SNP-major mode

Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read

Before frequency and genotyping pruning, there are 14 SNPs

27 founders and 13 non-founders found

Total genotyping rate in remaining individuals is 0.991071

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 14 SNPs

After filtering, 10 cases, 30 controls and 0 missing

After filtering, 21 males, 19 females, and 0 of unspecified sex

Writing pedigree information to [ ldp_tinywga.fam ] 

Writing map (extended format) information to [ ldp_tinywga.bim ] 

Writing genotype bitfile to [ ldp_tinywga.bed ] 

Using (default) SNP-major mode



Analysis finished: Wed May 19 15:15:38 2010







@----------------------------------------------------------@

|        PLINK!       |     v1.06      |   24/Apr/2009     |

|----------------------------------------------------------|

|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |

|----------------------------------------------------------|

|  For documentation, citation & bug-report instructions:  |

|        http://pngu.mgh.harvard.edu/purcell/plink/        |

@----------------------------------------------------------@



Skipping web check... [ --noweb ] 

Writing this text to log file [ tinywga.log ]

Analysis started: Wed May 19 15:15:38 2010



Options in effect:

	--noweb

	--bfile ldp_tinywga

	--het

	--out tinywga



Reading map (extended format) from [ ldp_tinywga.bim ] 

14 markers to be included from [ ldp_tinywga.bim ]

Reading pedigree information from [ ldp_tinywga.fam ] 

40 individuals read from [ ldp_tinywga.fam ] 

40 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

10 cases, 30 controls and 0 missing

21 males, 19 females, and 0 of unspecified sex

Reading genotype bitfile from [ ldp_tinywga.bed ] 

Detected that binary PED file is v1.00 SNP-major mode

Before frequency and genotyping pruning, there are 14 SNPs

27 founders and 13 non-founders found

Total genotyping rate in remaining individuals is 0.991071

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 14 SNPs

After filtering, 10 cases, 30 controls and 0 missing

After filtering, 21 males, 19 females, and 0 of unspecified sex



 **Warning** this analysis typically requires whole-genome level data

             to give accurate results 



Converting data to Individual-major format

Writing individual heterozygosity information to [ tinywga.het ] 



Analysis finished: Wed May 19 15:15:38 2010