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.nfs0000000165aa266100001f5e
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Lines total/split/realigned/skipped: 11461853/533423/542519/0
Lines total/split/realigned/skipped: 12278341/0/0/0
***** start general_preprocessing.py *****
input vcf name /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf
bgzip -c /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf > /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz
Bgzipping done
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz')
Tabixing done
('reheadering', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz')
('Reheadering', 'echo "UDN771219" | bcftools reheader -s - -o "/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz.tmp" "/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf.gz"')
('r_v_p_t', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz.tmp', 'r_v_p', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz')
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz')
Tabixing done
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz')
Tabixing done
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz')
Tabixing done
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz')
Tabixing done
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
Tabixing done
final vcf stored at : /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
final preprocessed vcf: /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
***** end general_preprocessing.py *****
-rw-rw----+ 1 ccurnin euan 742175924 Jan 12 23:00 /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz: VCF version 4.1 BGZF-compressed variant calling data
=============================================
vcfanno version 0.2.8 [built with go1.8]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 38 sources from 3 files
vcfanno.go:187: Info Error: AN_ASJ not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:187: Info Error: lua_start not found in header >> this error/warning may occur many times. reporting once here...
vcfanno.go:241: annotated 139 variants in 3.16 seconds (44.0 / second)
-rw-rw----+ 1 ccurnin euan 101698 Jan 12 23:02 /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf
the file should be run by typing the command in this exact manner:
python powerpoint_export.py excelSpreadsheetFilename UDNID
the excel spreadsheet must either be in the same directory as this piece of code or you must explicitly specify its filepath
make sure your excel filename doesnt have spaces! Spaces confuse linux
beginning export
powerpoint export finished, saving powerpoint file as /scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp-2/UDN771219_curationSlides.pptx
{'websearchAnnotations': ['omim', 'fathmm', 'mTaster', 'sift', 'phylop', 'mgi', 'rvis'], 'inputOrProbandBam': [], 'filtering': ['fbL'], 'alreadyGeneratedXls': [], 'debugArguments': [], 'udnId': ['UDN771219'], 'finalOutputDir': ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp-2/'], 'calling': ['rtg'], 'gcXls': ['/home/ccurnin/toAnnotate/ElM_PredictedDeleterious_HPO_output_forCharlie_Chloe_2.xlsx'], 'familyBams': [], 'familyFastqs': [], 'preprocessing': ['chP', 'rhP', 'smA', 'rmD'], 'familyVcfs': [], 'inputOrProbandFastq': [], 'variantListToFilterOn': [], 'runArchitecture': [], 'pedFile': [], 'inputOrProbandVcf': ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf'], 'annotation': ['exA', 'gnA', 'clV']}
('codeBaseDir, from', 'analysis_pipeline_master_script.py', 'to', '')
('preprocessingScriptPath', 'general_preprocessing.py')
('cwd', '/home/ccurnin/stmp4')
executing calling arguments: ['rtg']
('Executing the preprocessing arguments ', ['chP', 'rhP', 'smA', 'rmD'])
/home/ccurnin/stmp4
('Calling general_preprocessing.py', 'python general_preprocessing.py /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz smA chP rhP rmD False ')
('Preprocessing done', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
('Tabixing', 'tabix -f /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
('vcfs', ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167.vcf'])
('finalVCFs', ['/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz'])
single VCF
Step 2 done: currentWorkingVcf is /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
('Starting Step 3 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz')
filtering in main script /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
('Filtering fbL, output to', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf')
('Filtering on list from gcXls', 'UDN771219_variants.txt')
**START filter_vcf_by_variant_list**
filtering /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz
bcftools command: bcftools view /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz -R UDN771219_variants.txt -o /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
**END filter_vcf_by_variant_list**
new currentWorkingVcf/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf
('Starting Step 4 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf')
file="/scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz"
fields = ["AF_AFR", "AF_AMR", "AF_ASJ", "AF_EAS", "AF_FIN", "AF_NFE", "AF_OTH", "AF_SAS", "AN_AFR", "AN_AMR", "AN_ASJ", "AN_EAS", "AN_FIN", "AN_NFE", "AN_OTH", "AN_SAS", "AN_POPMAX", "AN_Female", "AN_Male", ]
ops=["first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first"]
file="/scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz"
fields = ["KG_AF_POPMAX", "ESP_AF_POPMAX", "clinvar_pathogenic", "KG_AF_GLOBAL", "KG_AC", "POPMAX", "AN_POPMAX", "AC_POPMAX", "AF", "AN", "AN_AFR", "AN_AMR", "AN_ASJ", "AN_EAS", "AN_FIN", "AN_NFE", "AN_OTH", "AN_SAS", ]
ops=["first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first","first"]
file="/scratch/PI/euan/common/stmpDatafiles/clinvar_20170905.vcf.gz"
fields = ["CLNSIG"]
ops=["first"]
('In directory', '/share/PI/euan/apps/stmp3/vcfanno')
('Running vcfanno', './vcfanno_linux64 -p 4 -lua /share/PI/euan/apps/stmp3/vcfanno/example/custom.lua /home/ccurnin/stmp4/myTestConfFile.toml /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf > /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf')
vcfanno done
('Running ls', 'ls -l /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf')
0
('Starting Step 5 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf')
('Starting Step 6 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf')
calling write_annotated_vcf_to_xls.vcf_to_xls
writing /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL_final_annotated_vcf.vcf to xls format
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Frequency among African/African American genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_AMR,Number=A,Type=Float,Description="Allele Frequency among Admixed American genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_ASJ,Number=A,Type=Float,Description="Allele Frequency among Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_EAS,Number=A,Type=Float,Description="Allele Frequency among East Asian genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_FIN,Number=A,Type=Float,Description="Allele Frequency among Finnish genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_NFE,Number=A,Type=Float,Description="Allele Frequency among Non-Finnish European genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_OTH,Number=A,Type=Float,Description="Allele Frequency among Other (population not assigned) genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AF_SAS,Number=A,Type=Float,Description="Allele Frequency among South Asian genotypes, for each ALT allele, in the same order as listed (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in 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'##INFO=<ID=AN_Female,Number=1,Type=Integer,Description="Total number of alleles in Female called genotypes (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AN_Male,Number=1,Type=Integer,Description="Total number of alleles in Male called genotypes (from /scratch/PI/euan/common/gnomad_data/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz)">\n', '##INFO=<ID=AN_NFE,Number=1,Type=Integer,Description="Non-Finnish European Chromosome Count (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=AN_OTH,Number=1,Type=Integer,Description="Other Chromosome Count (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=AN_POPMAX,Number=A,Type=String,Description="AN in the population with the max AF (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=AN_SAS,Number=1,Type=Integer,Description="South Asian Chromosome Count (from 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'##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n', '##INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">\n', '##INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">\n', '##INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium">\n', '##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">\n', '##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">\n', '##INFO=<ID=KG_AC,Number=A,Type=String,Description="Allele Count in 1000 Genomes (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=KG_AF_GLOBAL,Number=A,Type=String,Description="Overall allele frequency in 1000 Genomes (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=KG_AF_POPMAX,Number=A,Type=String,Description="Max allele frequency across populations in 1000 Genomes (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">\n', '##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">\n', '##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\n', '##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\n', '##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">\n', 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trained gaussian mixture model">\n', '##INFO=<ID=clinvar_pathogenic,Number=A,Type=String,Description="Clinvar Pathogenic Status (from /scratch/PI/euan/common/stmpDatafiles/ExAC.r0.3.1.sites.vep.vcf.gz)">\n', '##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">\n', '##INFO=<ID=lua_start_minus_2,Number=.,Type=Integer,Description="calculated field: lua_start_minus_2">\n', '##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">\n', '##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n', '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n', '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n', 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'##GATKCommandLine=<ID=ApplyRecalibration,Version=3.2-2-gec30cee,Date="Tue Nov 15 09:37:34 CST 2016",Epoch=1479224254397,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gpfs/gpfs1/levylab/genomes/gatk/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/gpfs/gpfs1/levylab/data/CLIA_vc/data_161114/merged/work/chroms_merged.vcf)] recal_file=(RodBinding name=recal_file source=/gpfs/gpfs1/levylab/data/CLIA_vc/data_161114/merged/work/filtered/work/snps.recal) tranches_file=/gpfs/gpfs1/levylab/data/CLIA_vc/data_161114/merged/work/filtered/work/snps.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=99.5 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n', '##GATKCommandLine=<ID=SelectVariants,Version=3.3-0-g37228af,Date="Fri Nov 18 14:22:06 CST 2016",Epoch=1479500526928,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gpfs/gpfs1/myerslab/reference/genomes/bwa-0.7.8/GRCh37.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/gpfs/gpfs1/levylab/data/UDN_vc/genotypes_161114.filtered.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sample_name=[C1011-HJ-0079] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n', '##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)\n', '##reference=file:///gpfs/gpfs1/myerslab/reference/genomes/bwa-0.7.8/GRCh37.fa\n', '##source=SelectVariants\n', '##bcftools_normVersion=1.4.1+htslib-1.4.1\n', '##bcftools_normCommand=norm --multiallelics - --check-ref x --fasta-ref=/share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP.vcf.gz; Date=Fri Jan 12 22:48:54 2018\n', '##bcftools_normCommand=norm -d both --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA.vcf.gz; Date=Fri Jan 12 22:54:01 2018\n', '##bcftools_annotateVersion=1.4.1+htslib-1.4.1\n', '##bcftools_annotateCommand=annotate --rename-chrs /scratch/PI/euan/common/udn/code/chromosome_notation.txt --output-type z --output /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD_chP.vcf.gz /scratch/PI/euan/common/udn/gateway/data/UDN771219/UDN771219-SL209167_rhP_smA_rmD.vcf.gz; Date=Fri Jan 12 22:57:32 2018\n', '##bcftools_viewVersion=1.4.1+htslib-1.4.1\n', '##bcftools_viewCommand=view -R UDN771219_variants.txt -o /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167_fbL.vcf /scratch/PI/euan/common/udn/gateway/data/UDN771219/preprocessed-UDN771219-SL209167.vcf.gz; Date=Fri Jan 12 23:01:57 2018\n', '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tUDN771219\n', '1\t12443036\t.\tC\tT\t700.3\tPASS\tAC=1;AF=0.0001483;AN=121412;BaseQRankSum=-1.716;ClippingRankSum=-0.015;DP=60;FS=0;GQ_MEAN=139.87;GQ_STDDEV=153.61;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.281;NCC=0;POSITIVE_TRAIN_SITE;QD=11.67;ReadPosRankSum=0.888;SOR=0.818;VQSLOD=16.93;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00017987;AF_OTH=0;AF_SAS=0;AN_AFR=10404;AN_AMR=11578;AN_ASJ=9776;AN_EAS=8654;AN_FIN=6614;AN_NFE=66504;AN_OTH=898;AN_SAS=16030;AN_POPMAX=66504;AN_Female=110822;AN_Male=134200;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=18\tGT:AD:DP:GQ:PL\t0/1:29,31:60:99:736,0,695\n', '1\t16902784\t.\tG\tT\t576.7\tVQSRTrancheSNP99.90to100.00\tAC=1;AF=0.002595,0.0004613;AN=121394;BaseQRankSum=-0.113;ClippingRankSum=0.272;DP=174;FS=5.921;GQ_MEAN=141.67;GQ_STDDEV=76.01;InbreedingCoeff=-0.0714;MQ=39.59;MQ0=0;MQRankSum=-1.572;NCC=0;QD=1.76;ReadPosRankSum=1.34;SOR=1.716;VQSLOD=-70.66;culprit=DP;AF_AFR=0.00056148,0;AF_AMR=0.00018855,0;AF_ASJ=0,0;AF_EAS=6.3243e-05,0;AF_FIN=0.00041498,4.6108e-05;AF_NFE=0.00088048,4.7852e-05;AF_OTH=0.00058525,0;AF_SAS=0.0002359,0;AN_AFR=9242;AN_AMR=11510;AN_ASJ=9472;AN_EAS=8638;AN_FIN=6530;AN_NFE=64374;AN_OTH=886;AN_SAS=16384;AN_POPMAX=9242,64374;AN_Female=104668;AN_Male=127662;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=AFR,NFE;AC_POPMAX=47,31\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:157,17:174:99:0|1:16902780_C_A:232,0,6367\n', '1\t19166377\t.\tC\tT\t496.3\tPASS\tAC=1;AF=5.765e-05;AN=121412;BaseQRankSum=1.55;ClippingRankSum=-0.451;DP=46;FS=0;GQ_MEAN=116.93;GQ_STDDEV=82.71;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.319;NCC=0;QD=10.79;ReadPosRankSum=1.24;SOR=0.693;VQSLOD=15.8;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0.00011596;AF_FIN=0;AF_NFE=4.476e-05;AF_OTH=0;AF_SAS=0.00022741;AN_AFR=10406;AN_AMR=11574;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6604;AN_NFE=66734;AN_OTH=906;AN_SAS=16512;AN_POPMAX=16512;AN_Female=111356;AN_Male=134900;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00023255814448930323;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=SAS;AC_POPMAX=4\tGT:AD:DP:GQ:PL\t0/1:22,24:46:99:532,0,413\n', '1\t145416614\t.\tG\tT\t486.3\tPASS\tAC=1;AF=0.000173;AN=121412;BaseQRankSum=-2.605;ClippingRankSum=-0.177;DP=44;FS=11.642;GQ_MEAN=121.87;GQ_STDDEV=98.89;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.884;NCC=0;POSITIVE_TRAIN_SITE;QD=11.05;ReadPosRankSum=1.36;SOR=0.407;VQSLOD=18.25;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00034023;AF_OTH=0.00018228;AF_SAS=0;AN_AFR=10402;AN_AMR=11576;AN_ASJ=9848;AN_EAS=8654;AN_FIN=6614;AN_NFE=66730;AN_OTH=908;AN_SAS=16512;AN_POPMAX=66730;AN_Female=111310;AN_Male=134868;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00046511628897860646;clinvar_pathogenic=1;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=21\tGT:AD:DP:GQ:PL\t0/1:20,24:44:99:522,0,477\n', '1\t156905823\t.\tG\tA\t443.3\tPASS\tAC=1;AF=0.0002389;AN=121412;BaseQRankSum=2.15;ClippingRankSum=-1.101;DP=49;FS=0;GQ_MEAN=121.07;GQ_STDDEV=99.42;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.61;NCC=0;QD=9.05;ReadPosRankSum=0.495;SOR=0.73;VQSLOD=15.24;culprit=MQRankSum;AF_AFR=0.00032671;AF_AMR=0.00074507;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00054647;AF_OTH=0.00036496;AF_SAS=0;AN_AFR=10400;AN_AMR=11554;AN_ASJ=9836;AN_EAS=8654;AN_FIN=6454;AN_NFE=66544;AN_OTH=902;AN_SAS=16118;AN_POPMAX=66544;AN_Female=111286;AN_Male=134802;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0.0005813953466713428;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=26\tGT:AD:DP:GQ:PL\t0/1:28,21:49:99:479,0,656\n', '1\t201338951\t.\tG\tA\t491.3\tPASS\tAC=1;AF=0.0001647;AN=121412;BaseQRankSum=4.89;ClippingRankSum=-1.552;DP=53;FS=0;GQ_MEAN=123.4;GQ_STDDEV=114.11;InbreedingCoeff=0.2611;MQ=60;MQ0=0;MQRankSum=-1.229;NCC=0;QD=9.27;ReadPosRankSum=-0.727;SOR=0.564;VQSLOD=13.58;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=2.9778e-05;AF_ASJ=0;AF_EAS=0.00028989;AF_FIN=0;AF_NFE=0.00020588;AF_OTH=0;AF_SAS=6.4973e-05;AN_AFR=10402;AN_AMR=11576;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66732;AN_OTH=904;AN_SAS=16512;AN_POPMAX=66732;AN_Female=111356;AN_Male=134904;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;clinvar_pathogenic=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=18\tGT:AD:DP:GQ:PL\t0/1:30,23:53:99:527,0,598\n', '1\t225607471\t.\tA\tG\t547.3\tPASS\tAC=1;AF=5.766e-05;AN=121410;BaseQRankSum=-2.174;ClippingRankSum=1.67;DP=49;FS=1.1;GQ_MEAN=127.87;GQ_STDDEV=108.49;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.172;NCC=0;QD=11.17;ReadPosRankSum=0.671;SOR=0.481;VQSLOD=15.28;culprit=MQRankSum;AF_AFR=0.00013072;AF_AMR=0;AF_ASJ=0;AF_EAS=5.7978e-05;AF_FIN=0;AF_NFE=0.00017922;AF_OTH=0;AF_SAS=0;AN_AFR=10382;AN_AMR=11574;AN_ASJ=9848;AN_EAS=8642;AN_FIN=6614;AN_NFE=66696;AN_OTH=908;AN_SAS=16502;AN_POPMAX=66696;AN_Female=111280;AN_Male=134756;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00011627907224465162;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=7\tGT:AD:DP:GQ:PL\t0/1:23,26:49:99:583,0,519\n', '1\t236758906\t.\tC\tT\t615.3\tPASS\tAC=1;AF=0.0001977;AN=121412;BaseQRankSum=4.51;ClippingRankSum=0.24;DP=53;FS=1.054;GQ_MEAN=135.2;GQ_STDDEV=98.26;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.774;NCC=0;POSITIVE_TRAIN_SITE;QD=11.61;ReadPosRankSum=-0.222;SOR=0.919;VQSLOD=14.8;culprit=DP;AF_AFR=0.00013072;AF_AMR=0.00029797;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00032306;AF_OTH=0.00018275;AF_SAS=0;AN_AFR=10388;AN_AMR=11554;AN_ASJ=9842;AN_EAS=8598;AN_FIN=6610;AN_NFE=66614;AN_OTH=906;AN_SAS=16498;AN_POPMAX=11554;AN_Female=111184;AN_Male=134686;KG_AF_POPMAX=0.00139999995008111;ESP_AF_POPMAX=0.0003488372021820396;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=AMR;AC_POPMAX=4\tGT:AD:DP:GQ:PL\t0/1:26,27:53:99:651,0,489\n', '2\t27601172\t.\tC\tG\t559.3\tPASS\tAC=1;AF=7.414e-05;AN=121398;BaseQRankSum=1.52;ClippingRankSum=0.933;DP=51;FS=1.083;GQ_MEAN=125.47;GQ_STDDEV=121.08;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.198;NCC=0;QD=10.97;ReadPosRankSum=1.14;SOR=0.488;VQSLOD=15.75;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00021053;AF_OTH=0.0001856;AF_SAS=0;AN_AFR=9966;AN_AMR=11462;AN_ASJ=9830;AN_EAS=8458;AN_FIN=6318;AN_NFE=65486;AN_OTH=878;AN_SAS=16452;AN_POPMAX=65486;AN_Female=104998;AN_Male=129290;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0.0003488372021820396;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=9\tGT:AD:DP:GQ:PL\t0/1:25,26:51:99:595,0,561\n', '2\t29293599\t.\tG\tA\t562.3\tPASS\tAC=1;AF=0.0001074;AN=121062;BaseQRankSum=-0.127;ClippingRankSum=0.354;DP=39;FS=2.747;GQ_MEAN=126.93;GQ_STDDEV=131.15;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.042;NCC=0;QD=14.42;ReadPosRankSum=-0.496;SOR=0.368;VQSLOD=15.34;culprit=ReadPosRankSum;AF_AFR=0.00013086;AF_AMR=8.9344e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00016119;AF_OTH=0;AF_SAS=0;AN_AFR=9760;AN_AMR=11564;AN_ASJ=9848;AN_EAS=8624;AN_FIN=6612;AN_NFE=66612;AN_OTH=894;AN_SAS=16512;AN_POPMAX=66612;AN_Female=111304;AN_Male=134876;KG_AF_POPMAX=0.0020000000949949026;ESP_AF_POPMAX=0.0003555344883352518;KG_AF_GLOBAL=0.0005990415229462087;KG_AC=3;POPMAX=NFE;AC_POPMAX=10\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:22,17:39:99:0|1:29293599_G_A:598,0,1131\n', '2\t43571360\t.\tT\tC\t405.3\tPASS\tAC=1;AF=0.000298;AN=120796;BaseQRankSum=-4.345;ClippingRankSum=0.058;DP=56;FS=1.029;GQ_MEAN=118.8;GQ_STDDEV=90.22;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.846;NCC=0;QD=7.24;ReadPosRankSum=0.534;SOR=0.747;VQSLOD=15.37;culprit=QD;AF_AFR=6.8503e-05;AF_AMR=0.00016818;AF_ASJ=0.00022407;AF_EAS=0;AF_FIN=0.00041073;AF_NFE=0.00057576;AF_OTH=0;AF_SAS=0;AN_AFR=7748;AN_AMR=7496;AN_ASJ=8926;AN_EAS=6908;AN_FIN=5242;AN_NFE=49192;AN_OTH=652;AN_SAS=12384;AN_POPMAX=49192;AN_Female=104060;AN_Male=125692;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00024295432376675308;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=31\tGT:AD:DP:GQ:PL\t0/1:30,26:56:99:441,0,710\n', '2\t98430726\t.\tA\tC\t481.3\tPASS\tAC=1;AF=3.31e-05;AN=120828;BaseQRankSum=-4.457;ClippingRankSum=-0.436;DP=53;FS=2.347;GQ_MEAN=126.73;GQ_STDDEV=108.33;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-2.215;NCC=0;QD=9.08;ReadPosRankSum=1.11;SOR=1.102;VQSLOD=15.41;culprit=MQRankSum;AF_AFR=0;AF_AMR=2.9794e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=9.8529e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9800;AN_AMR=11554;AN_ASJ=9846;AN_EAS=8626;AN_FIN=6614;AN_NFE=66698;AN_OTH=898;AN_SAS=16502;AN_POPMAX=66698;AN_Female=111276;AN_Male=134814;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00024265954561997205;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=4\tGT:AD:DP:GQ:PL\t0/1:26,27:53:99:517,0,619\n', '2\t179306432\t.\tC\tCAGTTTCCATAAATGACTCTAGCCTGCAAATTGTAGTATATTCTCTCTTA\t443.7\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.93;ClippingRankSum=0.309;DP=56;FS=2.263;GQ_MEAN=127.6;GQ_STDDEV=57.84;InbreedingCoeff=-0.0714;MQ=60;MQ0=0;MQRankSum=0.87;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.3;ReadPosRankSum=-3.672;SOR=1.044;VQSLOD=-5.197;culprit=ReadPosRankSum;AF_AFR=0,0,0,0,0,0;AF_AMR=0,0,0,2.9996e-05,0,2.9996e-05;AF_ASJ=0,0,0.00010227,0,0,0;AF_EAS=0,0,0,0,0,0;AF_FIN=0,0,4.4891e-05,4.4891e-05,0,0;AF_NFE=2.7008e-05,5.4016e-05,0,9.0027e-06,0,0;AF_OTH=0,0,0,0,0,0;AF_SAS=0,0,0,0,0,0;AN_AFR=15256;AN_AMR=33338;AN_ASJ=9778;AN_EAS=17156;AN_FIN=22276;AN_NFE=111078;AN_OTH=5442;AN_SAS=30712;AN_POPMAX=111078,111078,9778,22276,0,33338;AN_Female=110758;AN_Male=134278\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:45,11:56:99:0|1:179306432_C_CAGTTTCCATAAATGACTCTAGCCTGCAAATTGTAGTATATTCTCTCTTA:326,0,17285\n', '2\t179567166\t.\tT\tA\t533.3\tPASS\tAC=1;AF=0.0002069,8.275e-06;AN=120842;BaseQRankSum=-0.23;ClippingRankSum=-1.13;DP=49;FS=0;GQ_MEAN=131.8;GQ_STDDEV=120.99;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.05;NCC=0;QD=10.88;ReadPosRankSum=-0.39;SOR=0.622;VQSLOD=15.61;culprit=MQ;AF_AFR=6.5419e-05;AF_AMR=2.9781e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00044816;AF_OTH=0;AF_SAS=0;AN_AFR=9800;AN_AMR=11576;AN_ASJ=9838;AN_EAS=8626;AN_FIN=6614;AN_NFE=66644;AN_OTH=898;AN_SAS=16430;AN_POPMAX=66644,8626;AN_Female=111210;AN_Male=134806;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0.0006072382675483823,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=NFE,EAS;AC_POPMAX=25,1\tGT:AD:DP:GQ:PL\t0/1:25,24:49:99:569,0,617\n', '2\t179590139\t.\tT\tC\t589.3\tPASS\tAC=1;AF=0.0002152;AN=120834;BaseQRankSum=-3.14;ClippingRankSum=-0.823;DP=57;FS=1.007;GQ_MEAN=135.33;GQ_STDDEV=135.74;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.36;NCC=0;QD=10.34;ReadPosRankSum=2.81;SOR=0.656;VQSLOD=15.28;culprit=ReadPosRankSum;AF_AFR=6.6313e-05;AF_AMR=6.0518e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00043383;AF_OTH=0;AF_SAS=0;AN_AFR=7848;AN_AMR=7888;AN_ASJ=9482;AN_EAS=6082;AN_FIN=5632;AN_NFE=49592;AN_OTH=660;AN_SAS=8986;AN_POPMAX=49592;AN_Female=108408;AN_Male=131060;KG_AF_POPMAX=0.00139999995008111;ESP_AF_POPMAX=0.0006024096510373056;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=24\tGT:AD:DP:GQ:PL\t0/1:30,27:57:99:625,0,753\n', '2\t198352663\t.\tT\tC\t707.3\tPASS\tAC=1;AF=4.942e-05;AN=121408;BaseQRankSum=-2.04;ClippingRankSum=0.571;DP=67;FS=3.367;GQ_MEAN=143.53;GQ_STDDEV=166;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.93;NCC=0;QD=10.56;ReadPosRankSum=2.69;SOR=1.207;VQSLOD=15.37;culprit=MQRankSum;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,5.7978e-05;AF_FIN=4.4851e-05,0;AF_NFE=0.00013459,0;AF_OTH=0.00018275,0;AF_SAS=3.2495e-05,0;AN_AFR=10008;AN_AMR=11468;AN_ASJ=9844;AN_EAS=8618;AN_FIN=6574;AN_NFE=66082;AN_OTH=896;AN_SAS=16408;AN_POPMAX=66082;AN_Female=111206;AN_Male=134730;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00011630611697910354;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=5\tGT:AD:DP:GQ:PL\t0/1:35,32:67:99:743,0,856\n', 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'3\t122873827\t.\tA\tT\t564.3\tPASS\tAC=1;AF=0.0003459,1.647e-05;AN=121412;BaseQRankSum=2.29;ClippingRankSum=0.093;DP=41;FS=0;GQ_MEAN=116.13;GQ_STDDEV=71.2;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.384;NCC=0;POSITIVE_TRAIN_SITE;QD=13.76;ReadPosRankSum=0.622;SOR=0.542;VQSLOD=16.94;culprit=MQ;AF_AFR=0.00019603,0;AF_AMR=0,2.9778e-05;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=4.4899e-05,0;AF_NFE=0.00090421,8.9526e-06;AF_OTH=0.00036456,0;AF_SAS=0,3.2486e-05;AN_AFR=10406;AN_AMR=11578;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66730;AN_OTH=908;AN_SAS=16512;AN_POPMAX=66730,16512;AN_Female=111346;AN_Male=134878;KG_AF_POPMAX=0.0010000000474974513,0;ESP_AF_POPMAX=0.0008139534620568156,0;KG_AF_GLOBAL=0.00019968050764873624,0;KG_AC=1,0;POPMAX=NFE,SAS;AC_POPMAX=38,1\tGT:AD:DP:GQ:PL\t0/1:17,24:41:99:600,0,372\n', 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'4\t114468804\t.\tA\tG\t384.3\tPASS\tAC=1;AF=1.688e-05;AN=118474;BaseQRankSum=-2.874;ClippingRankSum=0.166;DP=52;FS=0;GQ_MEAN=119.6;GQ_STDDEV=83.76;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.55;NCC=0;QD=7.39;ReadPosRankSum=0.24;SOR=0.719;VQSLOD=15.08;culprit=QD;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.1802e-05;AF_OTH=0;AF_SAS=0;AN_AFR=2152;AN_AMR=1232;AN_ASJ=8852;AN_EAS=1594;AN_FIN=2318;AN_NFE=12864;AN_OTH=272;AN_SAS=7556;AN_POPMAX=NA;AN_Female=83536;AN_Male=102140;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NA;AC_POPMAX=NA\tGT:AD:DP:GQ:PL\t0/1:29,23:52:99:420,0,718\n', '4\t123277134\t.\tC\tT\t394.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=3.12;ClippingRankSum=0.719;DP=41;FS=9.155;GQ_MEAN=120.87;GQ_STDDEV=85.9;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.641;NCC=0;QD=9.62;ReadPosRankSum=0.379;SOR=1.099;VQSLOD=16.94;culprit=MQ\tGT:AD:DP:GQ:PL\t0/1:22,19:41:99:430,0,479\n', '5\t76358989\t.\tGA\tG\t948.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.068;ClippingRankSum=1.04;DP=59;FS=3.67;GQ_MEAN=159.33;GQ_STDDEV=224.67;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.312;NCC=0;QD=16.07;ReadPosRankSum=-0.646;SOR=1.274;VQSLOD=0.382;culprit=SOR\tGT:AD:DP:GQ:PL\t0/1:30,29:59:99:984,0,971\n', '5\t98205548\t.\tATTC\tA\t1137.3\tPASS\tAC=1;AF=9.062e-05;AN=121392;BaseQRankSum=0.034;ClippingRankSum=1.05;DP=63;FS=0;GQ_MEAN=171.87;GQ_STDDEV=277.05;InbreedingCoeff=-0.0345;MQ=60.33;MQ0=0;MQRankSum=0.529;NCC=0;QD=18.05;ReadPosRankSum=-0.172;SOR=0.648;VQSLOD=3.35;culprit=FS;AF_AFR=6.5608e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00014459;AF_OTH=0;AF_SAS=0;AN_AFR=9854;AN_AMR=10548;AN_ASJ=9814;AN_EAS=7922;AN_FIN=6350;AN_NFE=58934;AN_OTH=866;AN_SAS=15546;AN_POPMAX=58934;AN_Female=110726;AN_Male=134076;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0002423654805170372;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=10\tGT:AD:DP:GQ:PL\t0/1:32,31:63:99:1173,0,1453\n', '5\t125912806\t.\tG\tA\t450.3\tPASS\tAC=1;AF=0.0005189;AN=121412;BaseQRankSum=4.69;ClippingRankSum=-0.19;DP=38;FS=2.873;GQ_MEAN=114;GQ_STDDEV=51.3;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.833;NCC=0;QD=11.85;ReadPosRankSum=0.745;SOR=1.014;VQSLOD=15.78;culprit=MQ;AF_AFR=0;AF_AMR=8.9334e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0.0012108;AF_NFE=0.00074294;AF_OTH=0.00054685;AF_SAS=0.00055227;AN_AFR=10402;AN_AMR=11566;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66726;AN_OTH=908;AN_SAS=16508;AN_POPMAX=16508;AN_Female=111362;AN_Male=134908;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00046511628897860646;clinvar_pathogenic=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=SAS;AC_POPMAX=12\tGT:AD:DP:GQ:PL\t0/1:18,20:38:99:486,0,298\n', '5\t145543991\t.\tC\tG\t608.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.68;ClippingRankSum=-0.713;DP=56;FS=19.529;GQ_MEAN=135.87;GQ_STDDEV=132.95;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.926;NCC=0;QD=10.86;ReadPosRankSum=2.3;SOR=2.819;VQSLOD=14.09;culprit=SOR\tGT:AD:DP:GQ:PL\t0/1:28,28:56:99:644,0,615\n', '5\t146258203\t.\tG\tC\t517.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.836;ClippingRankSum=1.7;DP=64;FS=2.074;GQ_MEAN=120.87;GQ_STDDEV=122.37;InbreedingCoeff=-0.0385;MQ=60;MQ0=0;MQRankSum=-1.227;NCC=0;QD=8.08;ReadPosRankSum=1.12;SOR=1.001;VQSLOD=15.7;culprit=MQRankSum\tGT:AD:DP:GQ:PL\t0/1:35,29:64:99:553,0,719\n', '6\t489033\t.\tC\tT\t458.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.57;ClippingRankSum=0.5;DP=56;FS=5.691;GQ_MEAN=126.27;GQ_STDDEV=101.93;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.2;NCC=0;QD=8.18;ReadPosRankSum=1.78;SOR=1.615;VQSLOD=15.97;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=2.6858e-05;AF_OTH=0;AF_SAS=0;AN_AFR=15300;AN_AMR=33458;AN_ASJ=9850;AN_EAS=17240;AN_FIN=22292;AN_NFE=111700;AN_OTH=5474;AN_SAS=30732;AN_POPMAX=111700;AN_Female=111250;AN_Male=134796\tGT:AD:DP:GQ:PL\t0/1:33,23:56:99:494,0,778\n', '6\t31599756\t.\tG\tT\t453.3\tPASS\tAC=1;AF=8.499e-06;AN=117662;BaseQRankSum=-1.866;ClippingRankSum=-0.691;DP=48;FS=3.917;GQ_MEAN=121.47;GQ_STDDEV=102.33;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.27;NCC=0;QD=9.44;ReadPosRankSum=2.28;SOR=0.953;VQSLOD=15.77;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=4.6347e-05;AF_OTH=0;AF_SAS=0;AN_AFR=8878;AN_AMR=11406;AN_ASJ=9682;AN_EAS=8492;AN_FIN=6516;AN_NFE=62506;AN_OTH=848;AN_SAS=15484;AN_POPMAX=62506;AN_Female=107572;AN_Male=132842;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:24,24:48:99:489,0,538\n', '6\t32713127\t.\tG\tC\t36.6\tPASS\tAC=1;AF=0.0005602;AN=121376;BaseQRankSum=0.624;ClippingRankSum=0.208;DP=40;FS=8.397;GQ_MEAN=60.93;GQ_STDDEV=38.61;InbreedingCoeff=-0.1131;MQ=58.97;MQ0=0;MQRankSum=-2.362;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.47;ReadPosRankSum=-1.153;SOR=1.808;VQSLOD=-3.972;culprit=QD;AF_AFR=0.00020064;AF_AMR=0;AF_ASJ=0.00020375;AF_EAS=0;AF_FIN=0;AF_NFE=5.4268e-05;AF_OTH=0.00018349;AF_SAS=0;AN_AFR=9880;AN_AMR=11558;AN_ASJ=9816;AN_EAS=8610;AN_FIN=6614;AN_NFE=65344;AN_OTH=894;AN_SAS=16500;AN_POPMAX=9880;AN_Female=110276;AN_Male=134328;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=9\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:37,3:40:12:0|1:32713102_G_A:12,0,1587\n', '6\t32713128\t.\tG\tT\t36.5\tPASS\tAC=1;AF=0.0005602;AN=121376;BaseQRankSum=1.21;ClippingRankSum=0.4;DP=40;FS=8.473;GQ_MEAN=62.13;GQ_STDDEV=39.02;InbreedingCoeff=-0.113;MQ=58.97;MQ0=0;MQRankSum=-1.733;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.46;ReadPosRankSum=-1.438;SOR=1.802;VQSLOD=-3.762;culprit=QD;AF_AFR=0.00020048;AF_AMR=0;AF_ASJ=0.00020379;AF_EAS=0;AF_FIN=0;AF_NFE=6.3313e-05;AF_OTH=0.00018355;AF_SAS=0;AN_AFR=9880;AN_AMR=11556;AN_ASJ=9814;AN_EAS=8610;AN_FIN=6614;AN_NFE=65348;AN_OTH=894;AN_SAS=16498;AN_POPMAX=9880;AN_Female=110270;AN_Male=134304;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=9\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:37,3:40:12:0|1:32713102_G_A:12,0,1587\n', '6\t33377482\t.\tCTGTGTGTGTGTG\tC\t5138.4\tPASS\tAC=0;AF=0;AN=2;BaseQRankSum=0.229;ClippingRankSum=-0.102;DP=22;FS=1.227;GQ_MEAN=72.71;GQ_STDDEV=125.54;InbreedingCoeff=0.2881;MQ=60;MQ0=0;MQRankSum=0.406;NCC=1;QD=11.43;ReadPosRankSum=0.665;SOR=0.748;VQSLOD=0.424;culprit=InbreedingCoeff\tGT:AD:DP:GQ:PL\t0/0:0,0,3,11,8:22:99:1089,627,552\n', '6\t33377482\t.\tCTGTGTGTGTGTG\tC\t5138.4\tPASS\tAC=0;AF=0;AN=2;BaseQRankSum=0.229;ClippingRankSum=-0.102;DP=22;FS=1.227;GQ_MEAN=72.71;GQ_STDDEV=125.54;InbreedingCoeff=0.2881;MQ=60;MQ0=0;MQRankSum=0.406;NCC=1;QD=11.43;ReadPosRankSum=0.665;SOR=0.748;VQSLOD=0.424;culprit=InbreedingCoeff\tGT:AD:DP:GQ:PL\t0/0:0,0,3,11,8:22:99:1089,627,552\n', '6\t33411157\t.\tG\tC\t844.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.504;ClippingRankSum=-0.912;DP=55;FS=0;GQ_MEAN=112.87;GQ_STDDEV=79.07;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.81;NCC=0;QD=15.35;ReadPosRankSum=0.274;SOR=0.62;VQSLOD=14.4;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=8.9688e-06;AF_OTH=0;AF_SAS=0;AN_AFR=15248;AN_AMR=33574;AN_ASJ=9838;AN_EAS=17236;AN_FIN=22210;AN_NFE=111498;AN_OTH=5480;AN_SAS=30782;AN_POPMAX=111498;AN_Female=111042;AN_Male=134824\tGT:AD:DP:GQ:PL\t0/1:19,36:55:99:880,0,394\n', '6\t56365932\t.\tC\tA\t305.3\tPASS\tAC=1;AF=0.0001325;AN=120798;BaseQRankSum=0.117;ClippingRankSum=-0.317;DP=35;FS=5.023;GQ_MEAN=117.93;GQ_STDDEV=61.94;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.15;NCC=0;QD=8.72;ReadPosRankSum=1.72;SOR=0.924;VQSLOD=15.97;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00024211;AF_OTH=0;AF_SAS=0;AN_AFR=9776;AN_AMR=11304;AN_ASJ=9834;AN_EAS=8592;AN_FIN=6584;AN_NFE=66402;AN_OTH=884;AN_SAS=16388;AN_POPMAX=66402;AN_Female=111040;AN_Male=134578;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00036214388092048466;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=16\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:20,15:35:99:1|0:56365924_A_G:341,0,524\n', '6\t84896196\t.\tT\tC\t461.3\tPASS\tAC=1;AF=0.000486;AN=121404;BaseQRankSum=-1.019;ClippingRankSum=0.204;DP=50;FS=0;GQ_MEAN=127.73;GQ_STDDEV=102.36;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.37;NCC=0;QD=9.23;ReadPosRankSum=2.03;SOR=0.743;VQSLOD=15.07;culprit=ReadPosRankSum;AF_AFR=0.00058839;AF_AMR=8.9344e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=8.9726e-05;AF_NFE=0.0010216;AF_OTH=0.00018248;AF_SAS=0;AN_AFR=10398;AN_AMR=11578;AN_ASJ=9846;AN_EAS=8654;AN_FIN=6612;AN_NFE=66708;AN_OTH=906;AN_SAS=16508;AN_POPMAX=66708;AN_Female=111288;AN_Male=134812;KG_AF_POPMAX=0.001500000013038516;ESP_AF_POPMAX=0.00046511628897860646;KG_AF_GLOBAL=0.0005990415229462087;KG_AC=3;POPMAX=NFE;AC_POPMAX=50\tGT:AD:DP:GQ:PL\t0/1:26,24:50:99:497,0,605\n', '6\t131481327\t.\tA\tG\t423.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-2.083;ClippingRankSum=-0.467;DP=50;FS=1.088;GQ_MEAN=121.33;GQ_STDDEV=93.76;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.701;NCC=0;QD=8.47;ReadPosRankSum=-1.11;SOR=0.91;VQSLOD=13.54;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:27,23:50:99:459,0,649\n', '7\t26224871\t.\tG\tA\t527.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.58;ClippingRankSum=0.108;DP=37;FS=5.128;GQ_MEAN=115.67;GQ_STDDEV=57.12;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.851;NCC=0;QD=14.25;ReadPosRankSum=0.603;SOR=1.567;VQSLOD=16.28;culprit=MQ\tGT:AD:DP:GQ:PL\t0/1:15,22:37:99:563,0,322\n', '7\t26248176\t.\tG\tGC\t39.5\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.000404,3.298e-05;AN=121282;BaseQRankSum=1.52;ClippingRankSum=-0.432;DP=46;FS=1.429;GQ_MEAN=94.13;GQ_STDDEV=28.49;InbreedingCoeff=-0.0526;MQ=58.51;MQ0=0;MQRankSum=-2.884;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.86;ReadPosRankSum=-2.753;SOR=1.113;VQSLOD=-4.124;culprit=ReadPosRankSum;AF_AFR=0.00019955,0;AF_AMR=0,0;AF_ASJ=0,0.00010557;AF_EAS=0,0;AF_FIN=0,4.509e-05;AF_NFE=7.3109e-05,5.4832e-05;AF_OTH=0,0;AF_SAS=0,6.6863e-05;AN_AFR=9510;AN_AMR=11480;AN_ASJ=9472;AN_EAS=8584;AN_FIN=6594;AN_NFE=65432;AN_OTH=890;AN_SAS=16310;AN_POPMAX=9510,9510;AN_Female=108302;AN_Male=132152;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=AFR,AFR;AC_POPMAX=8,1\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:41,5:46:73:0|1:26248176_G_GC:73,0,5554\n', '7\t26248177\t.\tT\tTGACAAACC\t36.8\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.0002968,3.298e-05,4.123e-05;AN=121274;BaseQRankSum=2.57;ClippingRankSum=-0.023;DP=45;FS=2.045;GQ_MEAN=73.53;GQ_STDDEV=28.39;InbreedingCoeff=-0.0526;MQ=59.05;MQ0=0;MQRankSum=-0.933;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.31;ReadPosRankSum=-2.844;SOR=1.355;VQSLOD=-3.147;culprit=ReadPosRankSum;AF_AFR=0,0,0;AF_AMR=0,0,0;AF_ASJ=0.0001269,0,0;AF_EAS=0,0,0;AF_FIN=0,0,0;AF_NFE=2.9499e-05,0,9.8328e-06;AF_OTH=0,0,0;AF_SAS=3.7205e-05,0,0;AN_AFR=8958;AN_AMR=11360;AN_ASJ=7880;AN_EAS=8394;AN_FIN=6494;AN_NFE=63200;AN_OTH=856;AN_SAS=14644;AN_POPMAX=8958,63200,63200;AN_Female=99718;AN_Male=121368;KG_AF_POPMAX=0,0,0;ESP_AF_POPMAX=0,0,0;KG_AF_GLOBAL=0,0,0;KG_AC=0,0,0;POPMAX=AFR,NFE,NFE;AC_POPMAX=7,2,4\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:41,4:45:72:0|1:26248176_G_GC:72,0,5554\n', '7\t141756669\t.\tC\tA\t598.3\tPASS\tAC=1;AF=3.309e-05;AN=120898;BaseQRankSum=1.54;ClippingRankSum=0.854;DP=49;FS=0;GQ_MEAN=126.87;GQ_STDDEV=100.96;InbreedingCoeff=-0.0345;MQ=59.65;MQ0=0;MQRankSum=-1.9;NCC=0;NEGATIVE_TRAIN_SITE;QD=12.21;ReadPosRankSum=1.88;SOR=0.6;VQSLOD=-0.9351;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=5.3771e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9788;AN_AMR=11540;AN_ASJ=9848;AN_EAS=8574;AN_FIN=6612;AN_NFE=66668;AN_OTH=894;AN_SAS=16470;AN_POPMAX=66668;AN_Female=111252;AN_Male=134832;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00012062726455042139;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=4\tGT:AD:DP:GQ:PL\t0/1:22,27:49:99:634,0,491\n', '7\t151800292\t.\tA\tG\t330.3\tPASS\tAC=1;AF=0.0002306;AN=121412;BaseQRankSum=-1.921;ClippingRankSum=-0.895;DP=52;FS=0;GQ_MEAN=119.6;GQ_STDDEV=68.63;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.671;NCC=0;QD=6.35;ReadPosRankSum=-0.186;SOR=0.72;VQSLOD=15.07;culprit=QD;AF_AFR=6.5342e-05;AF_AMR=0.00017867;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00048337;AF_OTH=0;AF_SAS=0;AN_AFR=10404;AN_AMR=11570;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66720;AN_OTH=908;AN_SAS=16490;AN_POPMAX=66720;AN_Female=111360;AN_Male=134908;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0.0008139534620568156;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=25\tGT:AD:DP:GQ:PL\t0/1:31,21:52:99:366,0,687\n', '7\t154862950\t.\tG\tT\t332.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.18;ClippingRankSum=0.542;DP=41;FS=2.687;GQ_MEAN=110.6;GQ_STDDEV=72.36;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.125;NCC=0;QD=8.1;ReadPosRankSum=2.13;SOR=1.15;VQSLOD=16.31;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:24,17:41:99:368,0,557\n', '8\t8749671\t.\tC\tG\t588.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.385;ClippingRankSum=-0.311;DP=43;FS=2.67;GQ_MEAN=105;GQ_STDDEV=77.27;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.311;NCC=0;QD=13.68;ReadPosRankSum=1.43;SOR=0.374;VQSLOD=15.03;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.8001e-05;AF_OTH=0;AF_SAS=0;AN_AFR=15146;AN_AMR=33548;AN_ASJ=9814;AN_EAS=17214;AN_FIN=20140;AN_NFE=111102;AN_OTH=5454;AN_SAS=30774;AN_POPMAX=111102;AN_Female=109532;AN_Male=133660\tGT:AD:DP:GQ:PL\t0/1:17,26:43:99:624,0,380\n', '8\t27637697\t.\tT\tG\t419.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.765;ClippingRankSum=-1.176;DP=45;FS=0;GQ_MEAN=125.93;GQ_STDDEV=91.32;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.902;NCC=0;QD=9.32;ReadPosRankSum=1.22;SOR=0.653;VQSLOD=15.32;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=9.0243e-06;AF_OTH=0;AF_SAS=0;AN_AFR=15256;AN_AMR=33394;AN_ASJ=9794;AN_EAS=17114;AN_FIN=22284;AN_NFE=110812;AN_OTH=5450;AN_SAS=29766;AN_POPMAX=110812;AN_Female=110454;AN_Male=133416\tGT:AD:DP:GQ:PL\t0/1:25,20:45:99:455,0,596\n', '8\t38913232\t.\tA\tG\t743.3\tPASS\tAC=1;AF=8.237e-06;AN=121410;BaseQRankSum=0.485;ClippingRankSum=1.76;DP=61;FS=0.97;GQ_MEAN=135.6;GQ_STDDEV=126.87;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.962;NCC=0;QD=12.18;ReadPosRankSum=2.4;SOR=0.88;VQSLOD=14.94;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.7941e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10398;AN_AMR=11434;AN_ASJ=9842;AN_EAS=8642;AN_FIN=6584;AN_NFE=66610;AN_OTH=908;AN_SAS=16488;AN_POPMAX=66610;AN_Female=111188;AN_Male=134672;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:28,33:61:99:779,0,594\n', '8\t125081668\t.\tC\tCA\t940.3\tPASS\tAC=1;AF=1.655e-05;AN=120846;BaseQRankSum=0.869;ClippingRankSum=0.905;DP=54;FS=0;GQ_MEAN=128.07;GQ_STDDEV=113.37;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=2.28;NCC=0;QD=17.41;ReadPosRankSum=0.869;SOR=0.811;VQSLOD=1.15;culprit=FS;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=3.615e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9740;AN_AMR=11546;AN_ASJ=9794;AN_EAS=8584;AN_FIN=6614;AN_NFE=66600;AN_OTH=898;AN_SAS=16486;AN_POPMAX=66600;AN_Female=109850;AN_Male=133258;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:20,34:54:99:976,0,536\n', '8\t144511675\t.\tC\tT\t530.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.87;ClippingRankSum=0.03;DP=49;FS=2.434;GQ_MEAN=110.47;GQ_STDDEV=127.53;InbreedingCoeff=-0.0346;MQ=60;MQ0=0;MQRankSum=1.51;NCC=0;QD=10.82;ReadPosRankSum=0.89;SOR=0.387;VQSLOD=13.66;culprit=DP\tGT:AD:DP:GQ:PL\t0/1:25,24:49:99:566,0,594\n', '9\t2039776\t.\tACAGCAGCAG\tA\t4303.2\tPASS\tAC=0;AF=0;AN=2;BaseQRankSum=-0.377;ClippingRankSum=-0.225;DP=46;FS=2.144;GQ_MEAN=132.2;GQ_STDDEV=177.84;InbreedingCoeff=0.4374;MQ=60.34;MQ0=0;MQRankSum=0.193;NCC=0;QD=20.53;ReadPosRankSum=-0.415;SOR=0.502;VQSLOD=1.87;culprit=InbreedingCoeff;CLNSIG=Uncertain_significance\tGT:AD:DP:GQ:PL\t0/0:1,0,45:46:98:1796,1799,1838\n', '9\t4605352\t.\tT\tC\t488.3\tPASS\tAC=1;AF=4.965e-05;AN=120838;BaseQRankSum=-3.107;ClippingRankSum=-1.451;DP=63;FS=0.996;GQ_MEAN=125.4;GQ_STDDEV=110.86;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.248;NCC=0;QD=7.75;ReadPosRankSum=-0.134;SOR=0.478;VQSLOD=15.36;culprit=QD;AF_AFR=0;AF_AMR=2.9781e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=6.2671e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9790;AN_AMR=11540;AN_ASJ=9846;AN_EAS=8624;AN_FIN=6614;AN_NFE=66686;AN_OTH=898;AN_SAS=16498;AN_POPMAX=66686;AN_Female=111328;AN_Male=134884;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00024113817198667675;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=6\tGT:AD:DP:GQ:PL\t0/1:39,24:63:99:524,0,986\n', '9\t35906598\t.\tACCC\tA\t767.7\tPASS\tAC=0;AF=0.006968,0.0002452,9.429e-06,0.0006223,3.772e-05;AN=106052;BaseQRankSum=1.54;ClippingRankSum=1.33;DP=55;FS=5.339;GQ_MEAN=42.6;GQ_STDDEV=75.37;InbreedingCoeff=-0.2237;MQ=61.53;MQ0=0;MQRankSum=1.56;NCC=0;NEGATIVE_TRAIN_SITE;QD=21.33;ReadPosRankSum=-0.584;SOR=0.197;VQSLOD=-0.9931;culprit=SOR;KG_AF_POPMAX=0,NA,NA,NA,NA;ESP_AF_POPMAX=0.21732789278030396,NA,NA,NA,NA;KG_AF_GLOBAL=0,NA,NA,NA,NA;KG_AC=0,NA,NA,NA,NA;POPMAX=SAS,NFE,NA,AFR,AFR;AN_POPMAX=2398,11718,NA,1392,1392;AC_POPMAX=95,13,NA,23,1;AN_AFR=1392;AN_AMR=1858;AN_EAS=2146;AN_FIN=544;AN_NFE=11718;AN_OTH=104;AN_SAS=2398\tGT:AD:DP:GQ:PL\t0/0:55,0:55:0:0,0,628\n', '9\t35906601\t.\tC\tA\t1953.2\tVQSRTrancheINDEL99.00to99.90\tAC=0;AF=0;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.579;DP=23;FS=0.776;GQ_MEAN=84.93;GQ_STDDEV=98.77;InbreedingCoeff=0.2949;MQ=60;MQ0=0;MQRankSum=-0.656;NCC=0;NEGATIVE_TRAIN_SITE;QD=2.62;ReadPosRankSum=0.217;SOR=0.856;VQSLOD=-2.106;culprit=DP\tGT:AD:DP:GQ:PL\t0/0:20,0,3,0:23:99:347,409,1158\n', '9\t35906601\t.\tC\tCCCACCACACCCCTCACCACCTCCACCACCACCACCACCACCA\t1953.2\tVQSRTrancheINDEL99.00to99.90\tAC=0;AF=0;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.579;DP=23;FS=0.776;GQ_MEAN=84.93;GQ_STDDEV=98.77;InbreedingCoeff=0.2949;MQ=60;MQ0=0;MQRankSum=-0.656;NCC=0;NEGATIVE_TRAIN_SITE;QD=2.62;ReadPosRankSum=0.217;SOR=0.856;VQSLOD=-2.106;culprit=DP\tGT:AD:DP:GQ:PL\t0/0:20,0,3,0:23:99:347,409,1158\n', '9\t96019399\t.\tC\tT\t548.3\tPASS\tAC=1;AF=4.12e-05;AN=121368;BaseQRankSum=2.9;ClippingRankSum=0.939;DP=41;FS=1.193;GQ_MEAN=113.13;GQ_STDDEV=61.29;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.278;NCC=0;QD=13.37;ReadPosRankSum=2.32;SOR=0.919;VQSLOD=15.27;culprit=ReadPosRankSum;AF_AFR=0.00019965;AF_AMR=3.087e-05;AF_ASJ=0;AF_EAS=0.00017872;AF_FIN=0;AF_NFE=1.8496e-05;AF_OTH=0;AF_SAS=6.5445e-05;AN_AFR=9360;AN_AMR=11288;AN_ASJ=9628;AN_EAS=8518;AN_FIN=6010;AN_NFE=63252;AN_OTH=824;AN_SAS=16256;AN_POPMAX=9360;AN_Female=106980;AN_Male=131816;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00022696323867421597;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:17,24:41:99:584,0,329\n', '9\t114304465\t.\tG\tA\t512.3\tPASS\tAC=1;AF=1.647e-05;AN=121398;BaseQRankSum=3.67;ClippingRankSum=0.783;DP=45;FS=0;GQ_MEAN=123.4;GQ_STDDEV=95.85;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.237;NCC=0;QD=11.38;ReadPosRankSum=-0.284;SOR=0.622;VQSLOD=15.26;culprit=MQRankSum;AF_AFR=0.00019747;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.8058e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9736;AN_AMR=11524;AN_ASJ=9804;AN_EAS=8598;AN_FIN=6612;AN_NFE=66066;AN_OTH=896;AN_SAS=16436;AN_POPMAX=9736;AN_Female=110586;AN_Male=134350;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:23,22:45:99:548,0,468\n', '9\t125890531\t.\tC\tG\t657.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.51;ClippingRankSum=-0.616;DP=53;FS=2.417;GQ_MEAN=124.8;GQ_STDDEV=124.01;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.902;NCC=0;QD=12.4;ReadPosRankSum=0.17;SOR=1.232;VQSLOD=16.29;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=8.9686e-06;AF_OTH=0;AF_SAS=0;AN_AFR=15302;AN_AMR=33534;AN_ASJ=9846;AN_EAS=17244;AN_FIN=22300;AN_NFE=111500;AN_OTH=5476;AN_SAS=30778;AN_POPMAX=111500;AN_Female=111238;AN_Male=134742\tGT:AD:DP:GQ:PL\t0/1:24,29:53:99:693,0,570\n', '9\t134388668\t.\tC\tG\t524.4\tPASS\tAC=1;AF=0.003319,3.295e-05;AN=121408;BaseQRankSum=3.74;ClippingRankSum=-0.733;DP=42;FS=6.825;GQ_MEAN=108.07;GQ_STDDEV=65.21;InbreedingCoeff=-0.0417;MQ=60;MQ0=0;MQRankSum=-0.859;NCC=0;POSITIVE_TRAIN_SITE;QD=12.49;ReadPosRankSum=0.682;SOR=0.172;VQSLOD=17.86;culprit=MQ;AF_AFR=0.0377,0,0;AF_AMR=0.0016097,0,0;AF_ASJ=0,0,0;AF_EAS=0,0,0;AF_FIN=0,0,0;AF_NFE=9.0395e-05,3.6158e-05,9.0395e-06;AF_OTH=0.0011001,0,0;AF_SAS=0.00026009,0,0;AN_AFR=10008;AN_AMR=11386;AN_ASJ=9808;AN_EAS=8514;AN_FIN=5950;AN_NFE=65082;AN_OTH=850;AN_SAS=16270;AN_POPMAX=10008,65082;AN_Female=110236;AN_Male=134096;KG_AF_POPMAX=0.04390000179409981,0;ESP_AF_POPMAX=0.03245574235916138,0;clinvar_pathogenic=0,NA;KG_AF_GLOBAL=0.01218051090836525,0;KG_AC=61,0;POPMAX=AFR,NFE;AC_POPMAX=373,4\tGT:AD:DP:GQ:PL\t0/1:19,23:42:99:560,0,324\n', '9\t136633651\t.\tC\tG\t470.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-3.16;ClippingRankSum=-0.841;DP=47;FS=2.488;GQ_MEAN=120.53;GQ_STDDEV=107.08;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.181;NCC=0;QD=10.01;ReadPosRankSum=0.458;SOR=0.856;VQSLOD=15.52;culprit=MQRankSum\tGT:AD:DP:GQ:PL\t0/1:24,23:47:99:506,0,589\n', '9\t139396266\t.\tT\tG\t468.3\tPASS\tAC=1;AF=1.655e-05,8.274e-06;AN=120858;BaseQRankSum=1.53;ClippingRankSum=1.55;DP=46;FS=0;GQ_MEAN=124.27;GQ_STDDEV=105.33;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.02;NCC=0;QD=10.18;ReadPosRankSum=0.627;SOR=0.735;VQSLOD=15.61;culprit=MQ;AF_AFR=0,0;AF_AMR=0.00011918,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=4.5098e-05,9.0196e-06;AF_OTH=0.00018382,0;AF_SAS=0,0;AN_AFR=9358;AN_AMR=11424;AN_ASJ=9808;AN_EAS=8518;AN_FIN=6130;AN_NFE=64374;AN_OTH=850;AN_SAS=16462;AN_POPMAX=11424,64374;AN_Female=110344;AN_Male=134528;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=AMR,NFE;AC_POPMAX=2,1\tGT:AD:DP:GQ:PL\t0/1:24,22:46:99:504,0,535\n', '9\t139943392\t.\tC\tA\t548.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.187;ClippingRankSum=-0.331;DP=66;FS=0;GQ_MEAN=125.6;GQ_STDDEV=129.23;InbreedingCoeff=-0.0346;MQ=60;MQ0=0;MQRankSum=-0.253;NCC=0;QD=8.31;ReadPosRankSum=1.04;SOR=0.73;VQSLOD=15.77;culprit=MQ\tGT:AD:DP:GQ:PL\t0/1:38,28:66:99:584,0,884\n', '9\t139944752\t.\tA\tACCCGCCTGCC\t194.7\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.021;ClippingRankSum=0.778;DP=60;FS=0.878;GQ_MEAN=103.53;GQ_STDDEV=16.94;InbreedingCoeff=-0.0714;MQ=53.96;MQ0=0;MQRankSum=-4.758;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.6;ReadPosRankSum=-4.672;SOR=0.839;VQSLOD=-10.77;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:46,14,0:60:99:1|0:139944728_C_T:124,0,4013\n', '10\t323464\t.\tG\tA\t735.3\tPASS\tAC=1;AF=3.295e-05;AN=121412;BaseQRankSum=3.3;ClippingRankSum=0.037;DP=52;FS=0;GQ_MEAN=116.2;GQ_STDDEV=80.25;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.522;NCC=0;QD=14.14;ReadPosRankSum=0.354;SOR=0.793;VQSLOD=15.77;culprit=MQ;AF_AFR=6.5591e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0.00017408;AF_FIN=0;AF_NFE=3.5977e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10218;AN_AMR=11528;AN_ASJ=9812;AN_EAS=8616;AN_FIN=6612;AN_NFE=66336;AN_OTH=900;AN_SAS=16462;AN_POPMAX=8616;AN_Female=111012;AN_Male=134552;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=EAS;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:21,31:52:99:771,0,403\n', '10\t17156095\t.\tC\tT\t467.3\tPASS\tAC=1;AF=0.0003542,8.237e-06;AN=121408;BaseQRankSum=4.12;ClippingRankSum=-0.287;DP=46;FS=11.316;GQ_MEAN=123.27;GQ_STDDEV=97.53;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.478;NCC=0;POSITIVE_TRAIN_SITE;QD=10.16;ReadPosRankSum=0.419;SOR=0.982;VQSLOD=17.12;culprit=MQRankSum;AF_AFR=6.6216e-05,0;AF_AMR=0.00050856,0;AF_ASJ=0,0.00010221;AF_EAS=0,0;AF_FIN=4.5102e-05,0;AF_NFE=0.00041507,1.8047e-05;AF_OTH=0.00091811,0;AF_SAS=0.00075613,0;AN_AFR=9226;AN_AMR=10426;AN_ASJ=9784;AN_EAS=8116;AN_FIN=5952;AN_NFE=61610;AN_OTH=818;AN_SAS=14612;AN_POPMAX=14612,61610;AN_Female=110524;AN_Male=133802;KG_AF_POPMAX=0.003100000089034438,0;ESP_AF_POPMAX=0.0006976744043640792,0;KG_AF_GLOBAL=0.000798722030594945,0;KG_AC=4,0;POPMAX=SAS,NFE;AC_POPMAX=11,1\tGT:AD:DP:GQ:PL\t0/1:25,21:46:99:503,0,475\n', '10\t33015754\t.\tC\tT\t572.3\tPASS\tAC=1;AF=4.122e-05;AN=121292;BaseQRankSum=2.38;ClippingRankSum=1.06;DP=59;FS=0;GQ_MEAN=136.47;GQ_STDDEV=128.54;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.099;NCC=0;QD=9.7;ReadPosRankSum=-0.417;SOR=0.783;VQSLOD=15.13;culprit=MQ;AF_AFR=0,6.7186e-05;AF_AMR=0,6.283e-05;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0,2.784e-05;AF_OTH=0,0;AF_SAS=3.3679e-05,0;AN_AFR=9676;AN_AMR=11174;AN_ASJ=9544;AN_EAS=8420;AN_FIN=6544;AN_NFE=65014;AN_OTH=890;AN_SAS=16188;AN_POPMAX=9676;AN_Female=106998;AN_Male=130794;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:31,28:59:99:608,0,600\n', '10\t70056041\t.\tC\tG\t372.3\tPASS\tAC=1;AF=0.0004118;AN=121412;BaseQRankSum=1.08;ClippingRankSum=-0.688;DP=39;FS=4.773;GQ_MEAN=118;GQ_STDDEV=81.02;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.436;NCC=0;QD=9.55;ReadPosRankSum=0.913;SOR=0.234;VQSLOD=15.87;culprit=MQ;AF_AFR=0.00019646;AF_AMR=5.9655e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00077227;AF_OTH=0.00073099;AF_SAS=0.00042287;AN_AFR=9904;AN_AMR=11102;AN_ASJ=9828;AN_EAS=8542;AN_FIN=6316;AN_NFE=64604;AN_OTH=868;AN_SAS=15808;AN_POPMAX=64604;AN_Female=111074;AN_Male=134622;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00046511628897860646;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=43\tGT:AD:DP:GQ:PL\t0/1:20,19:39:99:408,0,459\n', '10\t91498735\t.\tC\tT\t431.3\tPASS\tAC=1;AF=4.942e-05;AN=121410;BaseQRankSum=-0.342;ClippingRankSum=-0.884;DP=44;FS=0;GQ_MEAN=125.73;GQ_STDDEV=94.59;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.106;NCC=0;QD=9.8;ReadPosRankSum=-1.426;SOR=0.722;VQSLOD=14.81;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=9.0108e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10374;AN_AMR=11512;AN_ASJ=9798;AN_EAS=8620;AN_FIN=6606;AN_NFE=66638;AN_OTH=906;AN_SAS=16482;AN_POPMAX=66638;AN_Female=110490;AN_Male=133910;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=6\tGT:AD:DP:GQ:PL\t0/1:24,20:44:99:467,0,580\n', '10\t95326494\t.\tC\tG\t722.3\tPASS\tAC=1;AF=2.497e-05;AN=120146;BaseQRankSum=2.95;ClippingRankSum=1.5;DP=69;FS=0;GQ_MEAN=138.8;GQ_STDDEV=171.18;InbreedingCoeff=-0.0345;MQ=59.66;MQ0=0;MQRankSum=-1.099;NCC=0;QD=10.47;ReadPosRankSum=-0.114;SOR=0.646;VQSLOD=-0.2132;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=8.059e-05;AF_OTH=0;AF_SAS=0;AN_AFR=4086;AN_AMR=6746;AN_ASJ=9048;AN_EAS=4754;AN_FIN=1976;AN_NFE=33584;AN_OTH=382;AN_SAS=7060;AN_POPMAX=33584;AN_Female=96928;AN_Male=122026;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00023457658244296908;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=3\tGT:AD:DP:GQ:PL\t0/1:36,33:69:99:758,0,756\n', '10\t101578700\t.\tCT\tC\t813.3\tPASS\tAC=1;AF=8.236e-06;AN=121412;BaseQRankSum=-1.743;ClippingRankSum=-0.066;DP=51;FS=2.422;GQ_MEAN=145.4;GQ_STDDEV=194.96;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.292;NCC=0;QD=15.95;ReadPosRankSum=-0.198;SOR=1.154;VQSLOD=1.18;culprit=SOR;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0,3.5901e-05;AF_OTH=0,0;AF_SAS=3.2489e-05,0;AN_AFR=10182;AN_AMR=11574;AN_ASJ=9838;AN_EAS=8638;AN_FIN=6614;AN_NFE=66710;AN_OTH=908;AN_SAS=16504;AN_POPMAX=66710;AN_Female=111204;AN_Male=134720;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:26,25:51:99:849,0,880\n', '10\t102107858\t.\tC\tG\t646.3\tPASS\tAC=1;AF=8.236e-06;AN=121412;BaseQRankSum=3.75;ClippingRankSum=1.52;DP=43;FS=1.267;GQ_MEAN=100.73;GQ_STDDEV=27.9;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.31;NCC=0;QD=15.03;ReadPosRankSum=0.505;SOR=0.555;VQSLOD=15.12;culprit=MQ;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=1.7953e-05,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=10372;AN_AMR=11576;AN_ASJ=9850;AN_EAS=8652;AN_FIN=6614;AN_NFE=66590;AN_OTH=908;AN_SAS=16506;AN_POPMAX=66590;AN_Female=111198;AN_Male=134702;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:14,29:43:99:682,0,191\n', '10\t114057917\t.\tC\tT\t525.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.54;ClippingRankSum=-0.165;DP=54;FS=0;GQ_MEAN=130.8;GQ_STDDEV=119.15;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.036;NCC=0;QD=9.73;ReadPosRankSum=1.19;SOR=0.693;VQSLOD=15.47;culprit=MQ\tGT:AD:DP:GQ:PL\t0/1:30,24:54:99:561,0,725\n', '11\t1016715\t.\tT\tC\t491.7\tVQSRTrancheSNP99.90to100.00\tAC=1;AF=0.000346;AN=121378;BaseQRankSum=0.84;ClippingRankSum=-0.57;DP=99;FS=23.18;GQ_MEAN=115.87;GQ_STDDEV=45.07;InbreedingCoeff=-0.1538;MQ=53.3;MQ0=0;MQRankSum=-1.358;NCC=0;QD=0.9;ReadPosRankSum=-0.351;SOR=4.003;VQSLOD=-234.6;culprit=DP;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0;AF_OTH=0;AF_SAS=0;AN_AFR=9996;AN_AMR=11448;AN_ASJ=9846;AN_EAS=8620;AN_FIN=6600;AN_NFE=66448;AN_OTH=898;AN_SAS=16498;AN_POPMAX=9996;AN_Female=111248;AN_Male=134732;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=4\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:92,7:99:87:0|1:1016715_T_C:87,0,3848\n', '11\t1016719\t.\tT\tG\t494.7\tVQSRTrancheSNP99.90to100.00\tAC=1;AF=0.0003378;AN=121378;BaseQRankSum=2.09;ClippingRankSum=-0.454;DP=104;FS=18.231;GQ_MEAN=116.93;GQ_STDDEV=43.28;InbreedingCoeff=-0.154;MQ=53.41;MQ0=0;MQRankSum=-0.391;NCC=0;QD=0.85;ReadPosRankSum=-1.556;SOR=3.558;VQSLOD=-220.6;culprit=DP;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0;AF_OTH=0;AF_SAS=0;AN_AFR=10006;AN_AMR=11502;AN_ASJ=9848;AN_EAS=8628;AN_FIN=6600;AN_NFE=66552;AN_OTH=902;AN_SAS=16504;AN_POPMAX=10006;AN_Female=111266;AN_Male=134764;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=4\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:93,11:104:99:0|1:1016715_T_C:111,0,3930\n', '11\t1017952\t.\tG\tT\t37.3\tVQSRTrancheSNP99.90to100.00\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.91;ClippingRankSum=-1.046;DP=178;FS=26.265;GQ_MEAN=116.87;GQ_STDDEV=12.14;InbreedingCoeff=-0.0345;MQ=48.32;MQ0=0;MQRankSum=-1.813;NCC=0;QD=0.21;ReadPosRankSum=1.49;SOR=4.545;VQSLOD=-190.6;culprit=DP;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=15304;AN_AMR=33576;AN_ASJ=9850;AN_EAS=17248;AN_FIN=22298;AN_NFE=111708;AN_OTH=5482;AN_SAS=30778;AN_POPMAX=0,0;AN_Female=111346;AN_Male=134898\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:164,14:178:73:0|1:1017949_G_A:73,0,6878\n', '11\t1026987\t.\tG\tA\t585.3\tPASS\tAC=1;AF=7.47e-05;AN=120474;BaseQRankSum=-0.903;ClippingRankSum=0.682;DP=52;FS=3.953;GQ_MEAN=122.67;GQ_STDDEV=94.32;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.51;NCC=0;QD=11.26;ReadPosRankSum=0.387;SOR=0.93;VQSLOD=15.6;culprit=MQRankSum;AF_AFR=0.00023515;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00016813;AF_OTH=0;AF_SAS=0;AN_AFR=4060;AN_AMR=3124;AN_ASJ=9340;AN_EAS=3300;AN_FIN=2558;AN_NFE=27942;AN_OTH=380;AN_SAS=9844;AN_POPMAX=4060;AN_Female=101408;AN_Male=123290;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00024078978458419442;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=AFR;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:23,29:52:99:621,0,463\n', '11\t1267817\t.\tG\tC\t469.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-2.49;ClippingRankSum=0.465;DP=40;FS=4.59;GQ_MEAN=108;GQ_STDDEV=76.97;InbreedingCoeff=-0.0345;MQ=59.14;MQ0=0;MQRankSum=0.41;NCC=0;NEGATIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-0.985;SOR=0.415;VQSLOD=-0.7081;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=8.9526e-06;AF_OTH=0;AF_SAS=0;AN_AFR=15300;AN_AMR=33578;AN_ASJ=9846;AN_EAS=17248;AN_FIN=22298;AN_NFE=111700;AN_OTH=5480;AN_SAS=30778;AN_POPMAX=111700;AN_Female=111340;AN_Male=134888\tGT:AD:DP:GQ:PL\t0/1:17,23:40:99:505,0,377\n', '11\t3059308\t.\tG\tA\t613.3\tPASS\tAC=1;AF=7.413e-05,5.765e-05,3.295e-05,8.236e-06;AN=121412;BaseQRankSum=3.52;ClippingRankSum=0.258;DP=52;FS=0;GQ_MEAN=121.07;GQ_STDDEV=86.45;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.221;NCC=0;QD=11.79;ReadPosRankSum=0.737;SOR=0.688;VQSLOD=15.92;culprit=MQ;AF_AFR=0.00019605,0.0011763,0,0;AF_AMR=0,0.00011917,0,0;AF_ASJ=0,0,0,0;AF_EAS=0,0,0,0;AF_FIN=0,0,0,0;AF_NFE=8.066e-05,0,4.4811e-05,0;AF_OTH=0,0,0,0;AF_SAS=3.2486e-05,0,0,0;AN_AFR=10406;AN_AMR=11578;AN_ASJ=9846;AN_EAS=8654;AN_FIN=6614;AN_NFE=66696;AN_OTH=908;AN_SAS=16416;AN_POPMAX=10406,10406,66696,66696;AN_Female=111294;AN_Male=134800;KG_AF_POPMAX=0,0,0,0;ESP_AF_POPMAX=0.00136239780113101,0,0,0;KG_AF_GLOBAL=0,0,0,0;KG_AC=0,0,0,0;POPMAX=AFR,AFR,NFE,NFE;AC_POPMAX=8,2,4,1\tGT:AD:DP:GQ:PL\t0/1:23,29:52:99:649,0,432\n', '11\t6644464\t.\tC\tT\t786.3\tPASS\tAC=1;AF=4.954e-05;AN=121104;BaseQRankSum=-0.582;ClippingRankSum=0.568;DP=62;FS=0.979;GQ_MEAN=134.6;GQ_STDDEV=130.85;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=2.2;NCC=0;QD=12.68;ReadPosRankSum=0.17;SOR=0.884;VQSLOD=14.14;culprit=MQRankSum;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0.00021489,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=5196;AN_AMR=4536;AN_ASJ=9050;AN_EAS=3582;AN_FIN=2808;AN_NFE=30778;AN_OTH=460;AN_SAS=10040;AN_POPMAX=30778;AN_Female=95812;AN_Male=115220;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00022727272880729288;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=5\tGT:AD:DP:GQ:PL\t0/1:27,35:62:99:822,0,607\n', '11\t32417885\t.\tG\tA\t378.3\tPASS\tAC=1;AF=0.00014;AN=121412;BaseQRankSum=-2.43;ClippingRankSum=0.379;DP=39;FS=1.236;GQ_MEAN=116.8;GQ_STDDEV=83.46;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.62;NCC=0;QD=9.7;ReadPosRankSum=2.8;SOR=0.644;VQSLOD=15.22;culprit=MQRankSum;AF_AFR=6.5342e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00041178;AF_OTH=0.00018228;AF_SAS=0;AN_AFR=10404;AN_AMR=11570;AN_ASJ=9850;AN_EAS=8650;AN_FIN=6614;AN_NFE=66696;AN_OTH=906;AN_SAS=16510;AN_POPMAX=66696;AN_Female=111354;AN_Male=134902;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00046522446791641414;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=16\tGT:AD:DP:GQ:PL\t0/1:20,19:39:99:414,0,491\n', '11\t66137005\t.\tT\tC\t522.3\tPASS\tAC=1;AF=2.471e-05;AN=121406;BaseQRankSum=-3.266;ClippingRankSum=1.78;DP=49;FS=1.114;GQ_MEAN=122.47;GQ_STDDEV=114.18;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.07;NCC=0;QD=10.66;ReadPosRankSum=0.131;SOR=0.461;VQSLOD=15.65;culprit=SOR;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=3.604e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10098;AN_AMR=11542;AN_ASJ=9822;AN_EAS=8592;AN_FIN=6612;AN_NFE=65610;AN_OTH=894;AN_SAS=16476;AN_POPMAX=65610;AN_Female=110670;AN_Male=134610;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=3\tGT:AD:DP:GQ:PL\t0/1:22,27:49:99:558,0,531\n', '11\t88300239\t.\tG\tA\t392.3\tPASS\tAC=1;AF=0.0001894;AN=121410;BaseQRankSum=1.04;ClippingRankSum=0.311;DP=40;FS=0;GQ_MEAN=118.73;GQ_STDDEV=86.66;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.879;NCC=0;QD=9.81;ReadPosRankSum=0.473;SOR=0.892;VQSLOD=15.6;culprit=MQ;AF_AFR=6.5394e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00032115;AF_OTH=0;AF_SAS=6.5634e-05;AN_AFR=10220;AN_AMR=11492;AN_ASJ=9656;AN_EAS=8556;AN_FIN=6576;AN_NFE=65380;AN_OTH=870;AN_SAS=13672;AN_POPMAX=65380;AN_Female=109756;AN_Male=132870;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.000348918343661353;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=21\tGT:AD:DP:GQ:PL\t0/1:20,20:40:99:428,0,452\n', '11\t102650052\t.\tC\tCT\t952.3\tPASS\tAC=1;AF=0.0003624;AN=121412;BaseQRankSum=0.758;ClippingRankSum=0.899;DP=49;FS=8.135;GQ_MEAN=140.2;GQ_STDDEV=151.57;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.535;NCC=0;QD=19.43;ReadPosRankSum=-0.313;SOR=0.98;VQSLOD=0.918;culprit=FS;AF_AFR=0.00026144;AF_AMR=0.00020856;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00076128;AF_OTH=0.0003647;AF_SAS=0;AN_AFR=10406;AN_AMR=11526;AN_ASJ=9850;AN_EAS=8652;AN_FIN=6614;AN_NFE=66732;AN_OTH=908;AN_SAS=16512;AN_POPMAX=66732;AN_Female=111318;AN_Male=134862;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0012115337885916233;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=38\tGT:AD:DP:GQ:PL\t0/1:21,28:49:99:988,0,687\n', '11\t103070158\t.\tA\tG\t461.3\tPASS\tAC=1;AF=0.0001242;AN=120764;BaseQRankSum=-1.538;ClippingRankSum=-0.747;DP=46;FS=1.145;GQ_MEAN=127.27;GQ_STDDEV=102.37;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.33;NCC=0;QD=10.03;ReadPosRankSum=0.176;SOR=0.583;VQSLOD=15.58;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00020925;AF_OTH=0;AF_SAS=0;AN_AFR=9012;AN_AMR=9740;AN_ASJ=9730;AN_EAS=7430;AN_FIN=6058;AN_NFE=59414;AN_OTH=804;AN_SAS=14318;AN_POPMAX=59414;AN_Female=110150;AN_Male=133040;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0005310674314387143;clinvar_pathogenic=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=15\tGT:AD:DP:GQ:PL\t0/1:23,23:46:99:497,0,543\n', '12\t6560489\t.\tG\tA\t426.3\tPASS\tAC=1;AF=4.942e-05;AN=121410;BaseQRankSum=0.509;ClippingRankSum=0.378;DP=41;FS=12.871;GQ_MEAN=123.47;GQ_STDDEV=95.5;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.404;NCC=0;QD=10.4;ReadPosRankSum=-0.248;SOR=2.518;VQSLOD=14.52;culprit=SOR;AF_AFR=6.5385e-05,0;AF_AMR=0,2.9787e-05;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0.00011717,0;AF_OTH=0.00018281,0;AF_SAS=0,0;AN_AFR=10324;AN_AMR=11562;AN_ASJ=9846;AN_EAS=8634;AN_FIN=6596;AN_NFE=66326;AN_OTH=892;AN_SAS=16506;AN_POPMAX=66326;AN_Female=110890;AN_Male=134558;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=6\tGT:AD:DP:GQ:PL\t0/1:21,20:41:99:462,0,499\n', '12\t7805403\t.\tC\tT\t599.3\tPASS\tAC=1;AF=0.0001154;AN=121346;BaseQRankSum=4.76;ClippingRankSum=0.45;DP=54;FS=0;GQ_MEAN=125.93;GQ_STDDEV=110.14;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.592;NCC=0;QD=11.1;ReadPosRankSum=-0.363;SOR=0.693;VQSLOD=14.98;culprit=MQRankSum;AF_AFR=0;AF_AMR=3.1644e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=9.3519e-05;AF_NFE=0.00019492;AF_OTH=0.00038685;AF_SAS=0;AN_AFR=9144;AN_AMR=11438;AN_ASJ=9234;AN_EAS=8396;AN_FIN=6586;AN_NFE=63328;AN_OTH=880;AN_SAS=15620;AN_POPMAX=63328;AN_Female=105604;AN_Male=129408;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0.00011630611697910354;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=11\tGT:AD:DP:GQ:PL\t0/1:27,27:54:99:635,0,520\n', '12\t10854602\t.\tC\tT\t977.3\tPASS\tAC=1;AF=0.0001071,8.236e-06;AN=121412;BaseQRankSum=4.68;ClippingRankSum=-0.569;DP=59;FS=7.16;GQ_MEAN=155.13;GQ_STDDEV=238.02;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.432;NCC=0;QD=16.56;ReadPosRankSum=-0.584;SOR=1.407;VQSLOD=15.95;culprit=ReadPosRankSum;AF_AFR=0,0;AF_AMR=0.00053757,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=5.3776e-05,8.9627e-06;AF_OTH=0.00036576,0;AF_SAS=0,0;AN_AFR=10406;AN_AMR=11578;AN_ASJ=9844;AN_EAS=8654;AN_FIN=6614;AN_NFE=66670;AN_OTH=908;AN_SAS=16456;AN_POPMAX=11578,66670;AN_Female=111222;AN_Male=134728;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=AMR,NFE;AC_POPMAX=11,1\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:30,29:59:99:0|1:10854602_C_T:1013,0,1061\n', '12\t53086339\t.\tC\tCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGGACCCAGGAGGCGGAGTTTGTAGTGA\t372.3\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.27;ClippingRankSum=-0.361;DP=38;FS=0;GQ_MEAN=114.2;GQ_STDDEV=82.29;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.68;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.47;ReadPosRankSum=-4.915;SOR=0.56;VQSLOD=-5.605;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:26,12:38:99:408,0,10036\n', '12\t71978399\t.\tC\tA\t707.3\tPASS\tAC=1;AF=0.0001318;AN=121412;BaseQRankSum=3.09;ClippingRankSum=-0.256;DP=66;FS=0;GQ_MEAN=141.27;GQ_STDDEV=153.03;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.757;NCC=0;POSITIVE_TRAIN_SITE;QD=10.72;ReadPosRankSum=-0.256;SOR=0.7;VQSLOD=16.42;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0.00010152;AF_EAS=0;AF_FIN=0;AF_NFE=0.00034912;AF_OTH=0.00018228;AF_SAS=0;AN_AFR=10406;AN_AMR=11578;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66736;AN_OTH=908;AN_SAS=16512;AN_POPMAX=66736;AN_Female=111354;AN_Male=134900;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0.0005813953466713428;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=16\tGT:AD:DP:GQ:PL\t0/1:33,33:66:99:743,0,694\n', '12\t81101681\t.\tT\tG\t224.3\tPASS\tAC=1;AF=8.237e-06,8.237e-06;AN=121410;BaseQRankSum=-0.306;ClippingRankSum=2.07;DP=45;FS=12.935;GQ_MEAN=106.33;GQ_STDDEV=44.05;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.091;NCC=0;QD=4.98;ReadPosRankSum=-1.41;SOR=1.642;VQSLOD=13.67;culprit=QD;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=8.9558e-06,8.9558e-06;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=10304;AN_AMR=11570;AN_ASJ=9850;AN_EAS=8644;AN_FIN=6612;AN_NFE=66492;AN_OTH=904;AN_SAS=16510;AN_POPMAX=66492,66492;AN_Female=111314;AN_Male=134884;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=NFE,NFE;AC_POPMAX=1,1\tGT:AD:DP:GQ:PL\t0/1:31,14:45:99:260,0,789\n', '13\t21729290\t.\tC\tCAGTTTTCTTTGTTGCTGACATCTCGGATGTTCTGTCCATGTTTAAGGAACCT\t722.7\tVQSRTrancheINDEL99.00to99.90\tAC=0;AF=0;AN=2;BaseQRankSum=0.619;ClippingRankSum=-0.008;DP=68;FS=0.844;GQ_MEAN=139.4;GQ_STDDEV=99.52;InbreedingCoeff=-0.0714;MQ=60;MQ0=0;MQRankSum=0.024;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.34;ReadPosRankSum=-5.304;SOR=0.56;VQSLOD=-6.97;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PGT:PID:PL\t0/0:56,0,12:68:99:0|1:21729252_T_C:374,546,3356\n', '13\t21734127\t.\tC\tCACTTTTTTCCAACTGCTGGATGATGGGGCTGGGAGTGGCAAAAACATTATCATTGAGCCTGGATTCTG\t836.7\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.76;ClippingRankSum=1.01;DP=66;FS=16.45;GQ_MEAN=146.27;GQ_STDDEV=140.48;InbreedingCoeff=-0.0714;MQ=60;MQ0=0;MQRankSum=-0.599;NCC=0;NEGATIVE_TRAIN_SITE;QD=0.27;ReadPosRankSum=-5.016;SOR=1.337;VQSLOD=-8.072;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:56,10:66:99:246,0,20386\n', '13\t21736016\t.\tT\tTTTTATTATTCCTC\t1000.0\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.27;ClippingRankSum=0.345;DP=60;FS=9.176;GQ_MEAN=157.27;GQ_STDDEV=114.14;InbreedingCoeff=-0.1111;MQ=60;MQ0=0;MQRankSum=-0.096;NCC=0;NEGATIVE_TRAIN_SITE;QD=1.53;ReadPosRankSum=-5.007;SOR=1.477;VQSLOD=-7.626;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:46,14:60:99:0|1:21736016_T_TTTTATTATTCCTC:445,0,19819\n', '13\t43788214\t.\tC\tT\t742.3\tPASS\tAC=1;AF=2.471e-05;AN=121412;BaseQRankSum=2.55;ClippingRankSum=-0.785;DP=62;FS=5.124;GQ_MEAN=127.6;GQ_STDDEV=103.07;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.7;NCC=0;QD=11.97;ReadPosRankSum=-0.87;SOR=0.934;VQSLOD=15.53;culprit=ReadPosRankSum;AF_AFR=6.5428e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=3.5905e-05;AF_OTH=0;AF_SAS=6.5206e-05;AN_AFR=10406;AN_AMR=11578;AN_ASJ=9840;AN_EAS=8654;AN_FIN=6614;AN_NFE=66696;AN_OTH=908;AN_SAS=16480;AN_POPMAX=16480;AN_Female=110964;AN_Male=134474;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=SAS;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:28,34:62:99:778,0,498\n', '13\t99907195\t.\tC\tA\t458.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.44;ClippingRankSum=0.704;DP=42;FS=6.641;GQ_MEAN=118.53;GQ_STDDEV=87.88;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.736;NCC=0;QD=10.91;ReadPosRankSum=2.14;SOR=1.041;VQSLOD=16.45;culprit=MQRankSum;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=8.9633e-06,5.378e-05;AF_OTH=0,0;AF_SAS=6.499e-05,0;AN_AFR=15304;AN_AMR=33574;AN_ASJ=9842;AN_EAS=17248;AN_FIN=22298;AN_NFE=111566;AN_OTH=5482;AN_SAS=30774;AN_POPMAX=30774,111566;AN_Female=111284;AN_Male=134804\tGT:AD:DP:GQ:PL\t0/1:21,21:42:99:494,0,433\n', '13\t111109205\t.\tC\tCTGCGTCTGCGTGGGACCCCAGGCGTCCGTGGGGCTGATGCCG\t97.7\tPASS\tAC=2;AF=0.0007324,4.882e-05,4.882e-05;AN=20482;DP=0;FS=0;GQ_MEAN=34.53;GQ_STDDEV=23.83;InbreedingCoeff=0.4205;MQ=59.43;MQ0=0;NCC=0;SOR=0.693;VQSLOD=1.25;culprit=FS;KG_AF_POPMAX=0,0,0;ESP_AF_POPMAX=0,0,0;KG_AF_GLOBAL=0,0,0;KG_AC=0,0,0;POPMAX=NFE,NFE,EAS;AN_POPMAX=4330,4330,366;AC_POPMAX=11,1,1;AN_AFR=678;AN_AMR=224;AN_EAS=366;AN_FIN=242;AN_NFE=4330;AN_OTH=152;AN_SAS=7262\tGT:AD:DP:GQ:PL\t1/1:0,0:0:6:137,6,0\n', '13\t114149939\t.\tG\tA\t545.3\tPASS\tAC=1;AF=4.122e-05;AN=121302;BaseQRankSum=4.69;ClippingRankSum=0.281;DP=59;FS=3.586;GQ_MEAN=127.8;GQ_STDDEV=125.82;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.483;NCC=0;QD=9.24;ReadPosRankSum=-1.21;SOR=0.76;VQSLOD=15.44;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0.00012191;AF_FIN=0;AF_NFE=4.056e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10206;AN_AMR=11474;AN_ASJ=6444;AN_EAS=8536;AN_FIN=6606;AN_NFE=63870;AN_OTH=792;AN_SAS=9396;AN_POPMAX=8536;AN_Female=97864;AN_Male=116072;KG_AF_POPMAX=0.0020000000949949026;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0.0003993610152974725;KG_AC=2;POPMAX=EAS;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:32,27:59:99:581,0,622\n', '14\t24045068\t.\tG\tA\t462.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.043;ClippingRankSum=0.775;DP=62;FS=5.204;GQ_MEAN=119.73;GQ_STDDEV=106.09;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.029;NCC=0;QD=7.46;ReadPosRankSum=-0.603;SOR=0.716;VQSLOD=15.68;culprit=QD\tGT:AD:DP:GQ:PL\t0/1:37,25:62:99:498,0,890\n', '14\t65241903\t.\tG\tA\t414.3\tPASS\tAC=1;AF=0.0004695;AN=121412;BaseQRankSum=4.47;ClippingRankSum=-0.303;DP=48;FS=4.181;GQ_MEAN=112.07;GQ_STDDEV=95.56;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.68;NCC=0;QD=8.63;ReadPosRankSum=-0.91;SOR=1.402;VQSLOD=16.4;culprit=ReadPosRankSum;AF_AFR=0.0001308,0;AF_AMR=0.00029781,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=8.9775e-05,0;AF_NFE=0.00079836,8.9704e-06;AF_OTH=0.00036496,0;AF_SAS=0.00045481,0;AN_AFR=10356;AN_AMR=11554;AN_ASJ=9846;AN_EAS=8610;AN_FIN=6614;AN_NFE=66406;AN_OTH=902;AN_SAS=16512;AN_POPMAX=66406;AN_Female=111158;AN_Male=134816;KG_AF_POPMAX=0.00139999995008111;ESP_AF_POPMAX=0.0005813953466713428;KG_AF_GLOBAL=0.0003993610152974725;KG_AC=2;POPMAX=NFE;AC_POPMAX=46\tGT:AD:DP:GQ:PL\t0/1:28,20:48:99:450,0,554\n', '15\t54804026\t.\tG\tA\t782.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.75;ClippingRankSum=1.35;DP=73;FS=6.113;GQ_MEAN=146.67;GQ_STDDEV=178.92;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.546;NCC=0;QD=10.72;ReadPosRankSum=2.63;SOR=0.698;VQSLOD=15.54;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:37,36:73:99:818,0,793\n', '15\t78894569\t.\tCTTTGGTCTT\tC\t1057.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-2.897;ClippingRankSum=0.364;DP=54;FS=0;GQ_MEAN=163.33;GQ_STDDEV=257.28;InbreedingCoeff=-0.0345;MQ=60.39;MQ0=0;MQRankSum=1.51;NCC=0;QD=6.53;ReadPosRankSum=-0.798;SOR=0.684;VQSLOD=1.4;culprit=FS\tGT:AD:DP:GQ:PL\t0/1:25,29:54:99:1093,0,2720\n', '15\t80415126\t.\tA\tC\t539.3\tPASS\tAC=1;AF=8.237e-06;AN=121410;BaseQRankSum=-1.859;ClippingRankSum=-0.009;DP=53;FS=0;GQ_MEAN=134.67;GQ_STDDEV=121.94;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.5;NCC=0;QD=10.17;ReadPosRankSum=0.294;SOR=0.627;VQSLOD=14.62;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=2.6923e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10354;AN_AMR=11548;AN_ASJ=9844;AN_EAS=8644;AN_FIN=6612;AN_NFE=66606;AN_OTH=904;AN_SAS=16476;AN_POPMAX=66606;AN_Female=111156;AN_Male=134656;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00023255814448930323;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:27,26:53:99:575,0,618\n', '15\t85400413\t.\tG\tA\t611.3\tPASS\tAC=1;AF=9.884e-05;AN=121406;BaseQRankSum=0.459;ClippingRankSum=0.909;DP=50;FS=5.957;GQ_MEAN=123.33;GQ_STDDEV=107.03;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.049;NCC=0;QD=12.23;ReadPosRankSum=0.205;SOR=0.223;VQSLOD=16.57;culprit=MQ;AF_AFR=0.00013098;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00012554;AF_OTH=0;AF_SAS=0;AN_AFR=10314;AN_AMR=11552;AN_ASJ=9840;AN_EAS=8648;AN_FIN=6580;AN_NFE=66100;AN_OTH=894;AN_SAS=16506;AN_POPMAX=66100;AN_Female=111150;AN_Male=134864;KG_AF_POPMAX=0.0010000000474974513;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=11\tGT:AD:DP:GQ:PL\t0/1:22,28:50:99:647,0,509\n', '16\t816650\t.\tC\tT\t418.3\tPASS\tAC=1;AF=0.0001494;AN=120478;BaseQRankSum=4.11;ClippingRankSum=-0.24;DP=48;FS=1.133;GQ_MEAN=117.8;GQ_STDDEV=93.77;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.031;NCC=0;QD=8.71;ReadPosRankSum=-0.868;SOR=0.46;VQSLOD=15.65;culprit=ReadPosRankSum;AF_AFR=6.5833e-05;AF_AMR=2.9788e-05;AF_ASJ=0;AF_EAS=0.00017412;AF_FIN=0;AF_NFE=0.00018937;AF_OTH=0.00018328;AF_SAS=0.00019498;AN_AFR=10134;AN_AMR=11540;AN_ASJ=9794;AN_EAS=8596;AN_FIN=6610;AN_NFE=65080;AN_OTH=882;AN_SAS=16498;AN_POPMAX=8596;AN_Female=110344;AN_Male=134532;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00022872826957609504;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=EAS;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:28,20:48:99:454,0,593\n', '16\t15045628\t.\tT\tC\t45.7\tVQSRTrancheSNP99.90to100.00\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.705;ClippingRankSum=1.88;DP=22;FS=9.379;GQ_MEAN=77.73;GQ_STDDEV=30.73;InbreedingCoeff=-0.0505;MQ=38.49;MQ0=0;MQRankSum=-1.175;NCC=0;QD=2.08;ReadPosRankSum=-1.175;SOR=3.407;VQSLOD=-19.27;culprit=MQ\tGT:AD:DP:GQ:PL\t0/1:17,5:22:81:81,0,420\n', '16\t30036507\t.\tG\tC\t595.3\tPASS\tAC=1;AF=5.557e-05;AN=35988;BaseQRankSum=2.06;ClippingRankSum=-0.22;DP=42;FS=0;GQ_MEAN=108.8;GQ_STDDEV=62.72;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.894;NCC=0;QD=14.17;ReadPosRankSum=0.505;SOR=0.838;VQSLOD=15.17;culprit=MQ;AF_AFR=0.00018077,0;AF_AMR=0,0.00017671;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0.00028307,0;AF_OTH=0.000516,0;AF_SAS=0,0;AN_AFR=388;AN_AMR=64;AN_ASJ=2598;AN_EAS=60;AN_FIN=4;AN_NFE=640;AN_OTH=18;AN_SAS=248;AN_POPMAX=NA;AN_Female=34276;AN_Male=38030;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NA;AC_POPMAX=NA\tGT:AD:DP:GQ:PL\t0/1:16,26:42:99:631,0,329\n', '16\t88789357\t.\tT\tG\t390.3\tPASS\tAC=1;AF=7.788e-05;AN=25680;BaseQRankSum=-1.546;ClippingRankSum=1.78;DP=47;FS=0;GQ_MEAN=115.4;GQ_STDDEV=87.99;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.1;NCC=0;QD=8.3;ReadPosRankSum=1.27;SOR=0.79;VQSLOD=15.5;culprit=MQ;AF_AFR=0,0;AF_AMR=0.00029279,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0.00048679,0;AF_NFE=0.00077112,1.836e-05;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=1486;AN_AMR=334;AN_ASJ=8150;AN_EAS=484;AN_FIN=30;AN_NFE=6060;AN_OTH=154;AN_SAS=7862;AN_POPMAX=6060;AN_Female=66444;AN_Male=78380;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:25,22:47:99:426,0,555\n', '17\t7139692\t.\tT\tC\t353.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.78;ClippingRankSum=-0.087;DP=43;FS=1.217;GQ_MEAN=116.47;GQ_STDDEV=76.53;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=2.32;NCC=0;QD=8.22;ReadPosRankSum=-1.379;SOR=1.061;VQSLOD=15.6;culprit=ReadPosRankSum\tGT:AD:DP:GQ:PL\t0/1:26,17:43:99:389,0,620\n', '17\t7760689\t.\tGC\tG\t490.3\tPASS\tAC=1;AF=8.237e-06,2.471e-05;AN=121404;BaseQRankSum=-0.167;ClippingRankSum=0.015;DP=37;FS=7.684;GQ_MEAN=120.8;GQ_STDDEV=113.47;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.988;NCC=0;NEGATIVE_TRAIN_SITE;QD=13.25;ReadPosRankSum=-0.714;SOR=2.133;VQSLOD=-0.7477;culprit=FS;AF_AFR=6.5703e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=6.3027e-05;AF_OTH=0;AF_SAS=0;AN_AFR=9648;AN_AMR=11536;AN_ASJ=9820;AN_EAS=8586;AN_FIN=6614;AN_NFE=65204;AN_OTH=880;AN_SAS=16368;AN_POPMAX=65204,65204;AN_Female=110502;AN_Male=134386;KG_AF_POPMAX=NA,0;ESP_AF_POPMAX=NA,0.00012115338176954538;KG_AF_GLOBAL=NA,0;KG_AC=NA,0;POPMAX=NFE,NFE;AC_POPMAX=1,3\tGT:AD:DP:GQ:PL\t0/1:19,18:37:99:526,0,557\n', '17\t18205701\t.\tG\tA\t573.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.287;ClippingRankSum=0.838;DP=46;FS=6.29;GQ_MEAN=123.73;GQ_STDDEV=104.34;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.57;NCC=0;QD=12.46;ReadPosRankSum=0.132;SOR=1.248;VQSLOD=16.32;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=8.9728e-06;AF_OTH=0;AF_SAS=0;AN_AFR=15290;AN_AMR=33524;AN_ASJ=9824;AN_EAS=17228;AN_FIN=22282;AN_NFE=111448;AN_OTH=5478;AN_SAS=30756;AN_POPMAX=111448;AN_Female=111128;AN_Male=134702\tGT:AD:DP:GQ:PL\t0/1:21,25:46:99:609,0,500\n', '17\t26715410\t.\tT\tG\t490.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.172;ClippingRankSum=2.1;DP=54;FS=0;GQ_MEAN=123.33;GQ_STDDEV=112.34;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.312;NCC=0;QD=9.08;ReadPosRankSum=1.36;SOR=0.713;VQSLOD=15.34;culprit=MQRankSum\tGT:AD:DP:GQ:PL\t0/1:31,23:54:99:526,0,734\n', '17\t28380680\t.\tA\tT\t594.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.265;ClippingRankSum=1.22;DP=48;FS=2.541;GQ_MEAN=124.2;GQ_STDDEV=87.02;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=2.02;NCC=0;QD=12.38;ReadPosRankSum=0.738;SOR=1.009;VQSLOD=14.63;culprit=MQRankSum\tGT:AD:DP:GQ:PL\t0/1:19,29:48:99:630,0,438\n', '17\t38975214\t.\tT\tTGCCGCCGTGGCCGCCGCTGGAGCTTCC\t485.1\tVQSRTrancheINDEL99.00to99.90\tAC=1;AF=0.014,6.154e-05;AN=16250;BaseQRankSum=0.298;ClippingRankSum=0.757;DP=29;FS=8.994;GQ_MEAN=91.07;GQ_STDDEV=124.33;InbreedingCoeff=-0.0645;MQ=61.3;MQ0=0;MQRankSum=1.26;NCC=0;NEGATIVE_TRAIN_SITE;QD=1.86;ReadPosRankSum=-1.354;SOR=2.285;VQSLOD=-1.864;culprit=FS;AF_AFR=0.0080091,0;AF_AMR=0.0211,8.5999e-05;AF_ASJ=0.014949,0;AF_EAS=0,0;AF_FIN=0.0255,0;AF_NFE=0.019443,0;AF_OTH=0.012913,0;AF_SAS=0.02,6.5522e-05;AN_AFR=202;AN_AMR=80;AN_ASJ=6288;AN_EAS=120;AN_FIN=88;AN_NFE=2382;AN_OTH=110;AN_SAS=6972;AN_POPMAX=6972,6972;AN_Female=29008;AN_Male=40974;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=SAS,SAS;AC_POPMAX=180,1\tGT:AD:DP:GQ:PL\t0/1:19,10:29:99:520,0,748\n', '17\t44143920\t.\tC\tT\t604.3\tPASS\tAC=1;AF=4.118e-05;AN=121410;BaseQRankSum=4.94;ClippingRankSum=-1.764;DP=57;FS=5.324;GQ_MEAN=129.07;GQ_STDDEV=109.62;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.14;NCC=0;QD=10.6;ReadPosRankSum=1.01;SOR=0.803;VQSLOD=15.39;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=6.3354e-05;AF_OTH=0;AF_SAS=0;AN_AFR=10374;AN_AMR=11466;AN_ASJ=9766;AN_EAS=8618;AN_FIN=6586;AN_NFE=66228;AN_OTH=888;AN_SAS=15668;AN_POPMAX=66228;AN_Female=110722;AN_Male=133876;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00011627907224465162;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=5\tGT:AD:DP:GQ:PL\t0/1:29,28:57:99:640,0,525\n', '17\t72860042\t.\tC\tT\t481.3\tPASS\tAC=1;AF=0.0001812;AN=121412;BaseQRankSum=1.3;ClippingRankSum=0.078;DP=50;FS=8.094;GQ_MEAN=121.67;GQ_STDDEV=109.83;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.35;NCC=0;QD=9.63;ReadPosRankSum=-0.993;SOR=0.964;VQSLOD=16.67;culprit=ReadPosRankSum;AF_AFR=6.5342e-05;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=4.4908e-05;AF_NFE=0.00032435;AF_OTH=0.0003655;AF_SAS=0;AN_AFR=10380;AN_AMR=11572;AN_ASJ=9812;AN_EAS=8644;AN_FIN=6614;AN_NFE=66286;AN_OTH=896;AN_SAS=16068;AN_POPMAX=66286;AN_Female=111046;AN_Male=134386;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.00046511628897860646;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=21\tGT:AD:DP:GQ:PL\t0/1:27,23:50:99:517,0,606\n', '18\t21406711\t.\tC\tG\t314.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-0.155;ClippingRankSum=1.04;DP=44;FS=0;GQ_MEAN=116.47;GQ_STDDEV=64.93;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.06;NCC=0;POSITIVE_TRAIN_SITE;QD=7.14;ReadPosRankSum=1.54;SOR=0.693;VQSLOD=16.73;culprit=QD;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=4.3146e-05,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=9984;AN_AMR=25796;AN_ASJ=8564;AN_EAS=12852;AN_FIN=16122;AN_NFE=69532;AN_OTH=4150;AN_SAS=24128;AN_POPMAX=69532,0;AN_Female=79228;AN_Male=91900\tGT:AD:DP:GQ:PL\t0/1:26,18:44:99:350,0,582\n', '19\t872114\t.\tG\tA\t274.3\tPASS\tAC=1;AF=0.0001584,8.337e-06;AN=119948;BaseQRankSum=0.308;ClippingRankSum=-0.178;DP=36;FS=5.439;GQ_MEAN=97.67;GQ_STDDEV=62.11;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.925;NCC=0;QD=7.62;ReadPosRankSum=-1.476;SOR=0.157;VQSLOD=14.16;culprit=ReadPosRankSum;AF_AFR=0.00027337,0;AF_AMR=0.00022114,0;AF_ASJ=0,0;AF_EAS=6.065e-05,0;AF_FIN=0,0;AF_NFE=0.00022658,9.4409e-06;AF_OTH=0.00097771,0;AF_SAS=0,3.3472e-05;AN_AFR=9252;AN_AMR=11080;AN_ASJ=9322;AN_EAS=8386;AN_FIN=5970;AN_NFE=61838;AN_OTH=816;AN_SAS=15364;AN_POPMAX=9252,61838;AN_Female=105120;AN_Male=129690;KG_AF_POPMAX=0.00139999995008111,0;ESP_AF_POPMAX=0.0004679457051679492,0;KG_AF_GLOBAL=0.00019968050764873624,0;KG_AC=1,0;POPMAX=AFR,NFE;AC_POPMAX=3,1\tGT:AD:DP:GQ:PL\t0/1:22,14:36:99:310,0,554\n', '19\t9968062\t.\tC\tT\t749.3\tPASS\tAC=1;AF=0.0002141;AN=121412;BaseQRankSum=1.39;ClippingRankSum=0.114;DP=64;FS=3.442;GQ_MEAN=138.2;GQ_STDDEV=145.07;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.047;NCC=0;QD=11.71;ReadPosRankSum=0.289;SOR=0.774;VQSLOD=15.71;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0.00017952;AF_NFE=0.00038512;AF_OTH=0.00018235;AF_SAS=0;AN_AFR=10380;AN_AMR=11562;AN_ASJ=9840;AN_EAS=8644;AN_FIN=6590;AN_NFE=66632;AN_OTH=904;AN_SAS=16512;AN_POPMAX=66632;AN_Female=111318;AN_Male=134856;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0003488372021820396;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=25\tGT:AD:DP:GQ:PL\t0/1:30,34:64:99:785,0,661\n', '19\t11040069\t.\tC\tT\t449.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=1.21;ClippingRankSum=-0.456;DP=50;FS=1.126;GQ_MEAN=120.8;GQ_STDDEV=101.28;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-2.398;NCC=0;QD=8.99;ReadPosRankSum=0.029;SOR=0.454;VQSLOD=15.02;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.8939e-05;AF_OTH=0;AF_SAS=0;AN_AFR=13982;AN_AMR=33148;AN_ASJ=9586;AN_EAS=16880;AN_FIN=19448;AN_NFE=105600;AN_OTH=5244;AN_SAS=30428;AN_POPMAX=105600;AN_Female=104450;AN_Male=129866\tGT:AD:DP:GQ:PL\t0/1:26,24:50:99:485,0,575\n', '19\t18343943\t.\tC\tA\t707.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.97;ClippingRankSum=0.503;DP=49;FS=0;GQ_MEAN=105.47;GQ_STDDEV=70.42;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.359;NCC=0;QD=14.43;ReadPosRankSum=0.256;SOR=0.657;VQSLOD=15.39;culprit=MQ;AF_AFR=0;AF_AMR=4.067e-05;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.6742e-05;AF_OTH=0;AF_SAS=0;AN_AFR=7902;AN_AMR=24588;AN_ASJ=8258;AN_EAS=11078;AN_FIN=15210;AN_NFE=59730;AN_OTH=3914;AN_SAS=23502;AN_POPMAX=24588;AN_Female=70426;AN_Male=83756\tGT:AD:DP:GQ:PL\t0/1:19,30:49:99:743,0,358\n', '19\t48184370\t.\tC\tT\t100.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.659;ClippingRankSum=-0.884;DP=39;FS=1.448;GQ_MEAN=92.67;GQ_STDDEV=23.02;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.338;NCC=0;QD=2.57;ReadPosRankSum=0.756;SOR=1.043;VQSLOD=14.83;culprit=QD;AF_AFR=0.0002061,0;AF_AMR=0.00019533,0;AF_ASJ=0,0;AF_EAS=0,0.00011312;AF_FIN=0,0;AF_NFE=0.0004056,0;AF_OTH=0.00033921,0;AF_SAS=0,5.3124e-05;AN_AFR=4852;AN_AMR=20478;AN_ASJ=5832;AN_EAS=8840;AN_FIN=4102;AN_NFE=36982;AN_OTH=2948;AN_SAS=18824;AN_POPMAX=36982,8840;AN_Female=45944;AN_Male=56914\tGT:AD:DP:GQ:PL\t0/1:29,10:39:99:136,0,653\n', '19\t49001133\t.\tGGGA\tG\t645.3\tPASS\tAC=1;AF=1.729e-05;AN=115704;BaseQRankSum=-1.588;ClippingRankSum=-0.48;DP=43;FS=9.057;GQ_MEAN=126.67;GQ_STDDEV=154.29;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=2.33;NCC=0;NEGATIVE_TRAIN_SITE;QD=15.01;ReadPosRankSum=1;SOR=1.367;VQSLOD=-0.9573;culprit=FS;AF_AFR=0,0;AF_AMR=8.6371e-05,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0,7.1788e-05;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=1160;AN_AMR=760;AN_ASJ=1676;AN_EAS=856;AN_FIN=342;AN_NFE=5722;AN_OTH=80;AN_SAS=1020;AN_POPMAX=NA;AN_Female=40658;AN_Male=47206;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NA;AC_POPMAX=NA\tGT:AD:DP:GQ:PGT:PID:PL\t0/1:25,18:43:99:0|1:49001122_C_A:681,0,1142\n', 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'19\t58199292\t.\tG\tA\t671.3\tPASS\tAC=1;AF=8.236e-06;AN=121412;BaseQRankSum=3.44;ClippingRankSum=0.44;DP=57;FS=3.783;GQ_MEAN=127.53;GQ_STDDEV=103.6;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.312;NCC=0;QD=11.78;ReadPosRankSum=1.53;SOR=0.304;VQSLOD=15.15;culprit=MQ;AF_AFR=0;AF_AMR=2.9781e-05;AF_ASJ=0;AF_EAS=5.7978e-05;AF_FIN=8.9694e-05;AF_NFE=6.2681e-05;AF_OTH=0.00018228;AF_SAS=0;AN_AFR=10404;AN_AMR=11576;AN_ASJ=9850;AN_EAS=8654;AN_FIN=6614;AN_NFE=66728;AN_OTH=908;AN_SAS=16512;AN_POPMAX=11576;AN_Female=111338;AN_Male=134884;KG_AF_POPMAX=0.00139999995008111;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=AMR;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:27,30:57:99:707,0,502\n', '20\t34057781\t.\tA\tG\t620.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=0.857;ClippingRankSum=-0.026;DP=54;FS=2.334;GQ_MEAN=128.93;GQ_STDDEV=130.74;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.684;NCC=0;QD=11.49;ReadPosRankSum=-1.203;SOR=1.179;VQSLOD=16.32;culprit=ReadPosRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=1.7913e-05;AF_OTH=0;AF_SAS=0;AN_AFR=15302;AN_AMR=33578;AN_ASJ=9844;AN_EAS=17246;AN_FIN=22300;AN_NFE=111648;AN_OTH=5480;AN_SAS=30772;AN_POPMAX=111648;AN_Female=111326;AN_Male=134844\tGT:AD:DP:GQ:PL\t0/1:26,28:54:99:656,0,600\n', '21\t34625019\t.\tA\tG\t667.3\tPASS\tAC=1;AF=0.0002224;AN=121412;BaseQRankSum=1.13;ClippingRankSum=-0.234;DP=49;FS=4.429;GQ_MEAN=126.6;GQ_STDDEV=87.87;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.824;NCC=0;QD=13.62;ReadPosRankSum=0.498;SOR=0.239;VQSLOD=15.44;culprit=MQ;AF_AFR=6.5351e-05,0;AF_AMR=2.9796e-05,0;AF_ASJ=0,0;AF_EAS=0,0;AF_FIN=0,0;AF_NFE=0.00059186,0;AF_OTH=0,0;AF_SAS=0,3.2522e-05;AN_AFR=10386;AN_AMR=11512;AN_ASJ=9846;AN_EAS=8644;AN_FIN=6600;AN_NFE=66566;AN_OTH=906;AN_SAS=16494;AN_POPMAX=66566;AN_Female=111254;AN_Male=134730;KG_AF_POPMAX=0.00139999995008111;ESP_AF_POPMAX=0.00046511628897860646;KG_AF_GLOBAL=0.00019968050764873624;KG_AC=1;POPMAX=NFE;AC_POPMAX=25\tGT:AD:DP:GQ:PL\t0/1:20,29:49:99:703,0,444\n', '22\t19978137\t.\tG\tA\t769.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=-1.558;ClippingRankSum=0.921;DP=69;FS=3.268;GQ_MEAN=135.8;GQ_STDDEV=159.83;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.608;NCC=0;QD=11.15;ReadPosRankSum=0.945;SOR=0.404;VQSLOD=15.64;culprit=MQ;AF_AFR=0,0;AF_AMR=3.0122e-05,0;AF_ASJ=0,0;AF_EAS=0,5.8432e-05;AF_FIN=0,0;AF_NFE=0,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=14220;AN_AMR=33198;AN_ASJ=9652;AN_EAS=17114;AN_FIN=20718;AN_NFE=107092;AN_OTH=5268;AN_SAS=29942;AN_POPMAX=33198,17114;AN_Female=106358;AN_Male=130846\tGT:AD:DP:GQ:PL\t0/1:32,37:69:99:805,0,712\n', '22\t20460112\t.\tTCCG\tT\t156.2\tPASS\tAC=2;AF=1;AN=2;DP=3;FS=0;GQ_MEAN=47.78;GQ_STDDEV=29.99;MQ=25;MQ0=0;NCC=6;NEGATIVE_TRAIN_SITE;QD=31.24;SOR=3.611;VQSLOD=-1.099;culprit=FS;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0;AF_OTH=0.00044563;AF_SAS=0;AN_AFR=8592;AN_AMR=13580;AN_ASJ=4766;AN_EAS=6516;AN_FIN=6434;AN_NFE=42614;AN_OTH=2244;AN_SAS=13844;AN_POPMAX=0;AN_Female=43902;AN_Male=54688\tGT:AD:DP:GQ:PL\t1/1:0,3:3:9:117,9,0\n', '22\t50962329\t.\tC\tT\t353.3\tPASS\tAC=1;AF=2.471e-05,8.236e-06;AN=121412;BaseQRankSum=3.18;ClippingRankSum=-0.769;DP=42;FS=2.652;GQ_MEAN=117.4;GQ_STDDEV=75.78;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=0.051;NCC=0;QD=8.41;ReadPosRankSum=0;SOR=1.013;VQSLOD=15.79;culprit=MQ;AF_AFR=0,0;AF_AMR=0,0;AF_ASJ=0,0;AF_EAS=0,5.7978e-05;AF_FIN=0,0;AF_NFE=4.4877e-05,0;AF_OTH=0,0;AF_SAS=0,0;AN_AFR=10370;AN_AMR=11566;AN_ASJ=9838;AN_EAS=8640;AN_FIN=6612;AN_NFE=66406;AN_OTH=904;AN_SAS=16510;AN_POPMAX=11566,8640;AN_Female=111194;AN_Male=134744;KG_AF_POPMAX=0,0;ESP_AF_POPMAX=0,0;KG_AF_GLOBAL=0,0;KG_AC=0,0;POPMAX=AMR,EAS;AC_POPMAX=1,1\tGT:AD:DP:GQ:PL\t0/1:25,17:42:99:389,0,547\n', 'X\t49061635\t.\tC\tT\t305.3\tPASS\tAC=1;AF=8.237e-05;AN=121408;BaseQRankSum=0.129;ClippingRankSum=0.776;DP=48;FS=19.442;GQ_MEAN=94.4;GQ_STDDEV=73.54;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.06;NCC=0;QD=6.36;ReadPosRankSum=1.14;SOR=3.379;VQSLOD=14.52;culprit=SOR;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00015105;AF_OTH=0;AF_SAS=0;AN_AFR=7914;AN_AMR=8790;AN_ASJ=7263;AN_EAS=6222;AN_FIN=3784;AN_NFE=43613;AN_OTH=557;AN_SAS=8723;AN_POPMAX=43613;AN_Female=111210;AN_Male=66347;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0001486325782025233;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=8\tGT:AD:DP:GQ:PL\t0/1:31,17:48:99:341,0,733\n', 'X\t110654142\t.\tC\tA\t558.3\tPASS\tAC=1;AF=8.237e-06;AN=121408;BaseQRankSum=-0.881;ClippingRankSum=0.898;DP=53;FS=3.91;GQ_MEAN=118.87;GQ_STDDEV=133.08;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-1.272;NCC=0;QD=10.53;ReadPosRankSum=0.827;SOR=0.314;VQSLOD=14.84;culprit=MQRankSum;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=5.0032e-05;AF_OTH=0;AF_SAS=0;AN_AFR=8514;AN_AMR=9318;AN_ASJ=7286;AN_EAS=6608;AN_FIN=4530;AN_NFE=47989;AN_OTH=633;AN_SAS=10124;AN_POPMAX=47989;AN_Female=111266;AN_Male=67269;KG_AF_POPMAX=0;ESP_AF_POPMAX=0;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=1\tGT:AD:DP:GQ:PL\t0/1:27,26:53:99:594,0,614\n', 'X\t130409472\t.\tG\tA\t569.3\tPASS\tAC=1;AF=1.647e-05;AN=121410;BaseQRankSum=1.02;ClippingRankSum=0.592;DP=44;FS=1.126;GQ_MEAN=106.73;GQ_STDDEV=91.9;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=-0.9;NCC=0;QD=12.94;ReadPosRankSum=0.071;SOR=0.686;VQSLOD=15;culprit=MQ;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0;AF_FIN=0;AF_NFE=0.00010062;AF_OTH=0;AF_SAS=0;AN_AFR=8506;AN_AMR=9314;AN_ASJ=7242;AN_EAS=6631;AN_FIN=4530;AN_NFE=47726;AN_OTH=621;AN_SAS=9188;AN_POPMAX=47726;AN_Female=111204;AN_Male=66694;KG_AF_POPMAX=0;ESP_AF_POPMAX=0.0001486325782025233;KG_AF_GLOBAL=0;KG_AC=0;POPMAX=NFE;AC_POPMAX=2\tGT:AD:DP:GQ:PL\t0/1:19,25:44:99:605,0,425\n', 'X\t153219786\t.\tC\tT\t335.3\tPASS\tAC=1;AF=0.5;AN=2;BaseQRankSum=2.52;ClippingRankSum=0.107;DP=51;FS=1.101;GQ_MEAN=94.6;GQ_STDDEV=79.61;InbreedingCoeff=-0.0345;MQ=60;MQ0=0;MQRankSum=1.63;NCC=0;QD=6.57;ReadPosRankSum=2.7;SOR=0.693;VQSLOD=13.38;culprit=DP;AF_AFR=0;AF_AMR=0;AF_ASJ=0;AF_EAS=0.00015823;AF_FIN=0;AF_NFE=1.3473e-05;AF_OTH=0;AF_SAS=0;AN_AFR=12118;AN_AMR=25582;AN_ASJ=6175;AN_EAS=12640;AN_FIN=15695;AN_NFE=74223;AN_OTH=3753;AN_SAS=16623;AN_POPMAX=12640;AN_Female=108408;AN_Male=58401\tGT:AD:DP:GQ:PL\t0/1:32,19:51:99:371,0,662\n']
infoDf initialized
Calling to_excel...
('xlsx data written to', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp-2/UDN771219_stmpAnnotatedOutput.xlsx')
('Starting Step 7 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp-2/UDN771219_stmpAnnotatedOutput.xlsx')
('Merging currentWorkingXls with', '/home/ccurnin/toAnnotate/ElM_PredictedDeleterious_HPO_output_forCharlie_Chloe_2.xlsx')
AF_EAS
('appending', 'AF_EAS')
AF_NFE
('appending', 'AF_NFE')
AF_SAS
('appending', 'AF_SAS')
AF_AMR
('appending', 'AF_AMR')
AF_AFR
('appending', 'AF_AFR')
NC
NI
NA
ESP_AF_POPMAX
('appending', 'ESP_AF_POPMAX')
KG_AF_POPMAX
('appending', 'KG_AF_POPMAX')
SD
SF
QUAL
('appending', 'QUAL')
ID
('appending', 'ID')
FILTER
('appending', 'FILTER')
GT
('appending', 'GT')
NJ
SX
GI
AN_AFR
('appending', 'AN_AFR')
AN_AMR
('appending', 'AN_AMR')
AN_ASJ
('appending', 'AN_ASJ')
AN_EAS
('appending', 'AN_EAS')
AN_FIN
('appending', 'AN_FIN')
AN_NFE
('appending', 'AN_NFE')
AN_OTH
('appending', 'AN_OTH')
AN_SAS
('appending', 'AN_SAS')
clinvar_pathogenic
('appending', 'clinvar_pathogenic')
KG_AF_GLOBAL
('appending', 'KG_AF_GLOBAL')
KG_AC
('appending', 'KG_AC')
POPMAX
('appending', 'POPMAX')
AN_POPMAX
('appending', 'AN_POPMAX')
AC_POPMAX
('appending', 'AC_POPMAX')
AF
('appending', 'AF')
AN
('appending', 'AN')
AN_Female
('appending', 'AN_Female')
AN_Male
('appending', 'AN_Male')
Chromosome Position Reference Allele \
0 1 12443036 C
1 1 16902784 G
2 1 19166377 C
3 1 145416614 G
4 1 156905823 G
5 1 201338951 G
6 1 225607471 A
7 1 236758906 C
8 2 27601172 C
9 2 29293599 G
10 2 43571360 T
11 2 98430726 A
12 2 179306432 C
13 2 179567166 T
14 2 179590139 T
15 2 198352663 T
16 2 219140307 C
17 2 220022915 C
18 2 231120221 C
19 2 241401875 C
20 2 241826521 T
21 2 242075315 T
22 X
23 $
24 3 44803004 G
25 3 52486222 G
26 3 122873827 A
27 3 182948795 G
28 4 8621131 A
29 4 39501825 G
.. ... ... ...
114 16 88789357 T
115 17 7139692 T
116 17 7760689 GC
117 17 7760689 GC
118 17 7760689 GC
119 17 18205701 G
120 17 26715410 T
121 17 28380680 A
122 17 38975214 T
123 17 44143920 C
124 17 72860042 C
125 18 21406711 C
126 19 872114 G
127 19 9968062 C
128 19 11040069 C
129 19 18343943 C
130 19 48184370 C
131 19 49001133 GGGA
132 19 49850479 G
133 19 58199292 G
134 20 34057781 A
135 21 34625019 A
136 22 19978137 G
137 22 20460112 TCCG
138 22 50962329 C
139 X 49061635 C
140
141 X 110654142 C
142 X 130409472 G
143 X 153219786 C
Sample Allele Variation Type \
0 T SNV
1 T SNV
2 T SNV
3 T SNV
4 A SNV
5 A SNV
6 G SNV
7 T SNV
8 G SNV
9 A SNV
10 C SNV
11 C SNV
12 CAGTTTCCATAAATGACTCTAGCCTGCAAATTGTAGTATATTCTCT... Insertion
13 A SNV
14 C SNV
15 C SNV
16 T SNV
17 T SNV
18 T SNV
19 T SNV
20 C SNV
21 C SNV
22 ´
23 ÷
24 T SNV
25 T SNV
26 T SNV
27 A SNV
28 C SNV
29 A SNV
.. ... ...
114 G SNV
115 C SNV
116 G Deletion
117 G Insertion
118 G Deletion
119 A SNV
120 G SNV
121 T SNV
122 TGCCGCCGTGGCCGCCGCTGGAGCTTCC Breakpoint
123 T SNV
124 T SNV
125 G SNV
126 A SNV
127 T SNV
128 T SNV
129 A SNV
130 T SNV
131 G Deletion
132 T SNV
133 A SNV
134 G SNV
135 G SNV
136 A SNV
137 T Deletion
138 T SNV
139 T SNV
140 ð
141 A SNV
142 A SNV
143 T SNV
Gene Region Gene Symbol \
0 Exonic VPS13D
1 Exonic NBPF10 (includes others)
2 Exonic TAS1R2
3 Exonic HFE2
4 Exonic ARHGEF11
5 Exonic; Intronic TNNT2
6 Exonic LBR
7 Exonic HEATR1
8 Exonic ZNF513
9 Exonic C2orf71
10 Exonic; ncRNA THADA
11 Exonic TMEM131
12 Splice Site PRKRA
13 Intronic TTN
14 Exonic; Intronic TTN
15 Promoter; Exonic HSPD1; SNORA105B
16 Exonic; Intronic; ncRNA PNKD; TMBIM1
17 Exonic NHEJ1
18 Intronic; Exonic SP140
19 Exonic GPC1
20 Exonic C2orf54
21 Exonic PASK
22
23
24 Promoter; Exonic KIAA1143; KIF15
25 Exonic TNNC1
26 ncRNA; Exonic PDIA5
27 Exonic MCF2L2
28 Exonic CPZ
29 Exonic UGDH
.. ... ...
114 Exonic PIEZO1
115 Promoter; Exonic DVL2; PHF23
116 Exonic KDM6B
117 Exonic KDM6B
118 Promoter; Exonic; Intronic NAA38; CYB5D1
119 Exonic TOP3A
120 Exonic SARM1
121 ncRNA; Exonic EFCAB5
122 Promoter; Exonic TMEM99; KRT10
123 Exonic KANSL1
124 Exonic; ncRNA FDXR
125 Exonic LAMA3
126 Exonic MED16
127 Exonic OLFM2
128 Promoter; Exonic YIPF2; TIMM29
129 Exonic PDE4C
130 Exonic BICRA
131 Exonic LMTK3
132 Exonic TEAD2
133 ncRNA; Exonic ZNF551
134 5'UTR; Exonic CEP250
135 Exonic IFNAR2
136 Exonic ARVCF
137 Exonic RIMBP3 (includes others)
138 Exonic; 3'UTR SCO2; NCAPH2
139 Exonic CACNA1F
140
141 Exonic; Intronic DCX
142 Exonic IGSF1
143 Exonic HCFC1
Transcript ID \
0 NM_015378.3; NM_018156.3
1 NM_017940.4
2 NM_152232.2
3 NM_202004.3; NM_001316767.1; NM_145277.4; NM_2...
4 NM_198236.2; NM_014784.3
5 NM_001001431.2; NM_001276347.1; NM_000364.3; N...
6 NM_002296.3; NM_194442.2
7 NM_018072.5
8 NM_144631.5; NM_001201459.1
9 NM_001029883.2
10 NM_022065.4; NM_001345924.1; NM_001083953.1; N...
11 NM_015348.1
12 NM_003690.4; NM_001139517.1; NM_001316362.1; N...
13 NM_001267550.2; NM_003319.4; NM_133432.3; NM_1...
14 NM_001267550.2; NM_003319.4; NM_133432.3; NM_1...
15 NR_132788.1; NM_002156.4; NM_199440.1
16 NM_015488.4; NM_001321436.1; NM_001321427.1; N...
17 NM_024782.2
18 NM_001278453.1; NM_001278452.1; NM_007237.4; N...
19 NM_002081.2
20 NM_001282921.1; NM_024861.3; NM_001085437.2
21 NM_001252120.1; NM_001252124.1; NM_001252122.1...
22
23
24 NM_020242.2; NM_001320334.1; NM_020696.3
25 NM_003280.2
26 NM_006810.3; NR_028444.1
27 NM_015078.3
28 NM_001014447.2; NM_001014448.2; NM_003652.3
29 NM_001184701.1; NM_003359.3; NM_001184700.1
.. ...
114 NM_001142864.3
115 NM_001284518.1; NM_024297.2; NM_004422.2; NM_0...
116 NM_001348716.1; NM_001080424.2
117 NM_001348716.1; NM_001080424.2
118 NM_144607.5; NM_032356.5; NM_001320924.2; NM_0...
119 NM_001320759.1; NM_004618.4
120 NM_015077.3
121 NM_198529.3; NR_026738.1; NM_001145053.1
122 NM_145274.3; NM_001195386.1; NM_000421.3; NM_0...
123 NM_001193465.1; NM_015443.3; NM_001193466.1
124 NM_001258013.3; NM_024417.4; NM_001258015.2; N...
125 NM_198129.2; NM_001127717.2
126 NM_005481.2
127 NM_001304348.1; NM_058164.3; NM_001304347.1
128 NM_138358.2; NM_001321440.1; NM_024029.4; NM_0...
129 NM_000923.5; NM_001330172.1
130 NM_015711.3
131 NM_001080434.1
132 NM_001256662.1; NM_001256660.1; NM_001256661.1...
133 NR_073102.1; NM_001270938.1; NM_138347.4
134 NM_001318219.1; NM_007186.5
135 NM_001289128.1; NM_207585.2; NM_001289125.1; N...
136 NM_001670.2
137 NM_015672.1
138 NM_001169110.1; NM_001169111.1; NM_152299.3; N...
139 NM_001256789.2; NM_001256790.2; NM_005183.3
140
141 NM_178153.2; NM_178151.2; NM_000555.3; NM_0011...
142 NM_001555.4; NM_001170961.1; NM_001170962.1
143 NM_005334.2
Transcript Variant \
0 c.11192C>T; c.11117C>T
1 c.2097A>C *
2 c.2236G>A
3 c.281G>T; c.620G>T; c.959G>T
4 c.4658C>T; c.4538C>T
5 c.53-1596C>T; c.68-1596C>T; c.90C>T
6 c.396T>C
7 c.1024G>A
8 c.680G>C; c.866G>C
9 c.3529C>T
10 c.4244A>G; c.4241A>G; c.4121A>G
11 c.1418T>G
12 c.515-2_515-1insTAAGAGAGAATATACTACAATTTGCAGGCT...
13 c.13657+35643A>T; c.13858+35643A>T; c.26701+15...
14 c.13282+12670A>G; c.17060A>G; c.19841A>G; c.13...
15 c.1488A>G; unknown
16 c.236+4035C>T; c.827G>A; c.494G>A
17 c.170G>A
18 c.1034C>T; c.872C>T; c.1214C>T; c.1159+2089C>T
19 c.593C>T
20 c.1310A>G; c.806A>G; c.863A>G
21 c.1172A>G; c.1277A>G
22
23
24 c.91C>A; c.-354G>T
25 c.102C>A
26 c.1283A>T
27 c.1873C>T
28 c.1746A>C; c.1713A>C; c.1335A>C
29 c.1132C>T; c.1222C>T; c.1423C>T
.. ...
114 c.4556A>C
115 c.353A>G; c.542A>G; c.554A>G; c.-2111A>G
116 c.786_791delACCACC
117 c.786_791dupACCACC
118 c.4-174delG; c.-763delC; c.81+11delG; c.52delG
119 c.691C>T; c.406C>T
120 c.1775T>G
121 c.1708A>T; c.1540A>T
122 TMEM99 - KRT10:A1573_A1755; KRT10:A1_A1573 - T...
123 c.1831G>A
124 c.994G>A; c.1168G>A; c.1150G>A; c.1243G>A; c.1...
125 c.2617C>G
126 c.1910C>T
127 c.223G>A; c.457G>A; c.529G>A
128 c.-839G>A; c.-913G>A; c.474C>T
129 c.59G>T
130 c.1943C>T
131 c.3277_3279delTCC
132 c.493C>A; c.886C>A; c.889C>A; c.877C>A
133 c.1565G>A; c.1649G>A
134 c.918A>G; c.-982A>G
135 c.593A>G
136 c.181C>T
137 c.1187_1189delCGG
138 c.512G>A; c.*525C>T
139 c.5896G>A; c.5863G>A; c.5701G>A
140
141 c.-22-494G>T; c.61G>T
142 c.3179C>T; c.3137C>T; c.3164C>T
143 c.4064G>A
Protein Variant ... \
0 p.A3731V; p.A3706V ...
1 p.Q699H ...
2 p.A746T ...
3 p.G94V; p.G207V; p.G320V ...
4 p.T1513I; p.T1553I ...
5 p.D30D ...
6 p.Y132Y ...
7 p.D342N ...
8 p.C289S; p.C227S ...
9 p.R1177W ...
10 p.Q1414R; p.Q1374R; p.Q1415R ...
11 p.L473R ...
12 NaN ...
13 NaN ...
14 p.N6931S; p.N6614S; p.N5687S ...
15 p.Q496Q ...
16 p.R165Q; p.R276Q ...
17 p.R57Q ...
18 p.S405F; p.S345F; p.S291F ...
19 p.A198V ...
20 p.Q269R; p.Q288R; p.Q437R ...
21 p.Q426R; p.Q391R ...
22 ...
23 ( ...
24 p.P31T ...
25 p.G34G ...
26 p.H428L ...
27 p.R625C ...
28 p.Q445H; p.Q582H; p.Q571H ...
29 p.P378S; p.P408S; p.P475S ...
.. ... ...
114 p.Q1519P ...
115 p.N118S; p.N181S; p.N185S ...
116 p.P263_P264del ...
117 p.P263_P264dup ...
118 p.A18fs*6 ...
119 p.P136S; p.P231S ...
120 p.F592C ...
121 p.R570*; p.R514* ...
122 TMEM99 - KRT10:S525_*585; KRT10:M1_S525 - TMEM... ...
123 p.V611I ...
124 p.E344K; p.E427K; p.E390K; p.E415K; p.E332K; p... ...
125 p.L873V ...
126 p.S637F ...
127 p.V75M; p.V153M; p.V177M ...
128 p.D158D ...
129 p.R20L ...
130 p.P648L ...
131 p.S1093del ...
132 p.P296T; p.P165T; p.P297T; p.P293T ...
133 p.R550Q; p.R522Q ...
134 p.I306M ...
135 p.D198G ...
136 p.P61S ...
137 p.A396del ...
138 p.R171Q ...
139 p.D1966N; p.D1955N; p.D1901N ...
140 ...
141 p.E21* ...
142 p.T1060I; p.T1046I; p.T1055I ...
143 p.R1355H ...
clinvar_pathogenic KG_AF_GLOBAL KG_AC POPMAX \
0 no value 0.00019968050764873624 1 NFE
1 no value 0,0 0,0 AFR,NFE
2 no value 0 0 SAS
3 1 0 0 NFE
4 no value 0.00019968050764873624 1 NFE
5 0 0 0 NFE
6 no value 0 0 NFE
7 no value 0.00019968050764873624 1 AMR
8 no value 0.00019968050764873624 1 NFE
9 no value 0.0005990415229462087 3 NFE
10 no value 0 0 NFE
11 no value 0 0 NFE
12 no value no value no value no value
13 no value 0,0 0,0 NFE,EAS
14 no value 0.00019968050764873624 1 NFE
15 no value 0 0 NFE
16 no value no value no value no value
17 no value 0 0 NFE
18 no value no value no value no value
19 no value 0.00019968050764873624 1 NFE
20 no value 0 0 NFE
21 no value 0 0 NFE
22 P
23 ° Æ
24 no value 0.00019968050764873624,0 1,0 NFE,NFE
25 no value no value no value no value
26 no value 0.00019968050764873624,0 1,0 NFE,SAS
27 no value 0 0 NFE
28 no value no value no value no value
29 no value 0.00019968050764873624 1 NFE
.. ... ... ... ...
114 no value 0 0 NFE
115 no value no value no value no value
116 no value NA,0 NA,0 NFE,NFE
117 no value NA,0 NA,0 NFE,NFE
118 no value NA,0 NA,0 NFE,NFE
119 no value no value no value no value
120 no value no value no value no value
121 no value no value no value no value
122 no value 0,0 0,0 SAS,SAS
123 no value 0 0 NFE
124 no value 0 0 NFE
125 no value no value no value no value
126 no value 0.00019968050764873624,0 1,0 AFR,NFE
127 no value 0 0 NFE
128 no value no value no value no value
129 no value no value no value no value
130 no value no value no value no value
131 no value 0 0 NaN
132 no value 0,0,0 0,0,0 NFE,NFE,AFR
133 no value 0.00019968050764873624 1 AMR
134 no value no value no value no value
135 no value 0.00019968050764873624 1 NFE
136 no value no value no value no value
137 no value no value no value no value
138 no value 0,0 0,0 AMR,EAS
139 no value 0 0 NFE
140
141 no value 0 0 NFE
142 no value 0 0 NFE
143 no value no value no value no value
AN_POPMAX AC_POPMAX \
0 66504 18
1 9242,64374 47,31
2 16512 4
3 66730 21
4 66544 26
5 66732 18
6 66696 7
7 11554 4
8 65486 9
9 66612 10
10 49192 31
11 66698 4
12 111078,111078,9778,22276,0,33338 no value
13 66644,8626 25,1
14 49592 24
15 66082 5
16 17234 no value
17 66708 26
18 111404 no value
19 42376 30
20 66708 30
21 66676 24
22 P G
23
24 65458,65458 29,1
25 no value no value
26 66730,16512 38,1
27 66602 8
28 no value no value
29 66664 51
.. ... ...
114 6060 2
115 no value no value
116 65204,65204 1,3
117 65204,65204 1,3
118 65204,65204 1,3
119 111448 no value
120 no value no value
121 no value no value
122 6972,6972 180,1
123 66228 5
124 66286 21
125 69532,0 no value
126 9252,61838 3,1
127 66632 25
128 105600 no value
129 24588 no value
130 36982,8840 no value
131 NaN NaN
132 66708,66708,10404 4,1,1
133 11576 1
134 111648 no value
135 66566 25
136 33198,17114 no value
137 0 no value
138 11566,8640 1,1
139 43613 8
140 à
141 47989 1
142 47726 2
143 12640 no value
AF AN AN_Female AN_Male
0 0.0001483 121412 110822 134200
1 0.002595,0.0004613 121394 104668 127662
2 5.765e-05 121412 111356 134900
3 0.000173 121412 111310 134868
4 0.0002389 121412 111286 134802
5 0.0001647 121412 111356 134904
6 5.766e-05 121410 111280 134756
7 0.0001977 121412 111184 134686
8 7.414e-05 121398 104998 129290
9 0.0001074 121062 111304 134876
10 0.000298 120796 104060 125692
11 3.31e-05 120828 111276 134814
12 0.5 2 110758 134278
13 0.0002069,8.275e-06 120842 111210 134806
14 0.0002152 120834 108408 131060
15 4.942e-05 121408 111206 134730
16 0.5 2 111054 134560
17 0.0002224 121412 111350 134904
18 0.5 2 111198 134674
19 0.0003257 119748 100038 125804
20 0.0002481 120902 110594 134268
21 0.0002059 121412 111344 134904
22
23
24 0.00028,8.236e-06 121412 110972 134512
25 0.5 2 no value no value
26 0.0003459,1.647e-05 121412 111346 134878
27 7.413e-05 121412 111142 134614
28 0.5 2 no value no value
29 0.000486 121408 111086 134452
.. ... ... ... ...
114 7.788e-05 25680 66444 78380
115 0.5 2 no value no value
116 8.237e-06,2.471e-05 121404 110502 134386
117 8.237e-06,2.471e-05 121404 110502 134386
118 8.237e-06,2.471e-05 121404 110502 134386
119 0.5 2 111128 134702
120 0.5 2 no value no value
121 0.5 2 no value no value
122 0.014,6.154e-05 16250 29008 40974
123 4.118e-05 121410 110722 133876
124 0.0001812 121412 111046 134386
125 0.5 2 79228 91900
126 0.0001584,8.337e-06 119948 105120 129690
127 0.0002141 121412 111318 134856
128 0.5 2 104450 129866
129 0.5 2 70426 83756
130 0.5 2 45944 56914
131 1.729e-05 115704 40658 47206
132 3.295e-05,1.647e-05,3.295e-05 121412 110464 134214
133 8.236e-06 121412 111338 134884
134 0.5 2 111326 134844
135 0.0002224 121412 111254 134730
136 0.5 2 106358 130846
137 1 2 43902 54688
138 2.471e-05,8.236e-06 121412 111194 134744
139 8.237e-05 121408 111210 66347
140
141 8.237e-06 121408 111266 67269
142 1.647e-05 121410 111204 66694
143 0.5 2 108408 58401
[144 rows x 73 columns]
('Starting Step 8 with', '/scratch/PI/euan/common/udn/gateway/data/UDN771219/stmp-2/UDN771219_merged.xlsx')
('Annotating with websearchAnnotations', ['omim', 'fathmm', 'mTaster', 'sift', 'phylop', 'mgi', 'rvis'])
0
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=VPS13D&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=VPS13D')
1
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=NBPF10 (includes others)&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=NBPF10 (includes others)')
2
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TAS1R2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TAS1R2')
3
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HFE2&chromosome=any&cm=&coordinate=&coordUnit=bp')
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4
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ARHGEF11&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ARHGEF11')
5
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TNNT2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TNNT2')
6
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=LBR&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=LBR')
7
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HEATR1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HEATR1')
8
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ZNF513&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ZNF513')
9
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=C2orf71&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=C2orf71')
10
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=THADA&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=THADA')
11
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TMEM131&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TMEM131')
12
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PRKRA&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PRKRA')
13
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TTN&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TTN')
14
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TTN&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TTN')
15
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HSPD1; SNORA105B&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HSPD1; SNORA105B')
16
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PNKD; TMBIM1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PNKD; TMBIM1')
17
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=NHEJ1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=NHEJ1')
18
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=SP140&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=SP140')
19
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=GPC1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=GPC1')
20
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=C2orf54&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=C2orf54')
21
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PASK&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PASK')
22
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=nan&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=nan')
23
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=nan&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=nan')
24
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=KIAA1143; KIF15&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=KIAA1143; KIF15')
25
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=TNNC1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=TNNC1')
26
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PDIA5&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PDIA5')
27
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=MCF2L2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=MCF2L2')
28
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CPZ&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CPZ')
29
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=UGDH&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=UGDH')
30
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CAMK2D&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CAMK2D')
31
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=KIAA1109&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=KIAA1109')
32
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=AGGF1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=AGGF1')
33
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CHD1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CHD1')
34
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ALDH7A1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ALDH7A1')
35
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=LARS&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=LARS')
36
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PPP2R2B&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PPP2R2B')
37
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=EXOC2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=EXOC2')
38
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=PRRC2A&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=PRRC2A')
39
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HLA-DQA2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HLA-DQA2')
40
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HLA-DQA2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HLA-DQA2')
41
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=KIFC1; PHF1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=KIFC1; PHF1')
42
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=KIFC1; PHF1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=KIFC1; PHF1')
43
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=SYNGAP1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=SYNGAP1')
44
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=DST&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=DST')
45
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CEP162&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CEP162')
46
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=AKAP7&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=AKAP7')
47
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=NFE2L3&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=NFE2L3')
48
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CBX3&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CBX3')
49
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CBX3&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CBX3')
50
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=MGAM&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=MGAM')
51
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=GALNT11&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=GALNT11')
52
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HTR5A; HTR5A-AS1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HTR5A; HTR5A-AS1')
53
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=MFHAS1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=MFHAS1')
54
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ESCO2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ESCO2')
55
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ADAM9&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ADAM9')
56
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=FER1L6&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=FER1L6')
57
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=MAFA&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=MAFA')
58
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=SMARCA2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=SMARCA2')
59
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=SPATA6L&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=SPATA6L')
60
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=HRCT1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=HRCT1')
61
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=WNK2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=WNK2')
62
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ZNF483&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ZNF483')
63
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=STRBP&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=STRBP')
64
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=POMT1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=POMT1')
65
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=VAV2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=VAV2')
66
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=NOTCH1&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=NOTCH1')
67
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ENTPD2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ENTPD2')
68
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=ENTPD2&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=ENTPD2')
69
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=DIP2C&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=DIP2C')
70
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CUBN&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CUBN')
71
('Opening', u'http://www.informatics.jax.org/allele/report.txt?phenotype=&nomen=CCDC7&chromosome=any&cm=&coordinate=&coordUnit=bp')
('Opening', u'http://genic-intolerance.org/Search?query=CCDC7')
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