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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>short_ Achab catch</title>
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<body><div class="META"><b>Arguments:</b><br>--vcf /home/tg/TOOLS/Captain-ACHAB/INPUT_hg19_multianno_MPA.vcf --case B00GMSH --dad B00GMSI --mum B00GMSJ --addCaseDepth --addCaseAB --outPrefix short --genemap2File genemap2.txt <br><br><br><b>VCF Header:</b><br>##fileformat=VCFv4.2
##GATKCommandLine.HaplotypeCaller=ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Wed Aug 01 04:38:56 CEST 2018",Epoch=1533091136036,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/MERGED_SAMPLES.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/HaplotypeCaller-1-sg/temp_01_of_28/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null 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 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/HaplotypeCaller-1-sg/temp_01_of_28/MERGED_SAMPLES.raw.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/home/guignardt/work-mobidic/nenufaar/refData/dbSNP/138/CORRECT_dbsnp_138.hg19.vcf.gz) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ReadPosRankSumTest] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=10 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=1 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
##GATKCommandLine.VariantFiltration=ID=VariantFiltration,Version=3.8-0-ge9d806836,Date="Wed Aug 01 05:16:32 CEST 2018",Epoch=1533093392176,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/VariantFiltration-1-sg/temp_01_of_28/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.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 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false 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 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.polyx.vcf) mask=(RodBinding name= source=UNBOUND) out=/lustre/guignardt/output/28658/AJI_Fam8/MERGED_SAMPLES/559/DIR_DRMAA/VariantFiltration-1-sg/temp_01_of_28/MERGED_SAMPLES.raw.polyx.gatk.vcf filterExpression=[DP 20, QUAL 30.0, QD 1.5, FS 60.000, MQ 10.00, POLYX 7] filterName=[LowCoverage, LowQual, LowQD, StrandBias, LowMappingQuality, R8] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
##VCFPolyXCmdLine=-R /home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa -o output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.polyx.vcf output/28658/AJI_Fam8/MERGED_SAMPLES/559/MERGED_SAMPLES.raw.vcf
##VCFPolyXHtsJdkHome=lib/com/github/samtools/htsjdk/2.6.1/htsjdk-2.6.1.jar
##VCFPolyXHtsJdkVersion=2.6.1
##VCFPolyXVersion=ff2326c651be81dd8b99173a69d6005b274ca4c6
##bcftools_normCommand=norm -O v -m - -o /mnt/data/MobiDL/captainAchab/Done/B00GMSH/CaptainAchab/B00GMSH.vcf /home/adminngs/autoAchab/cromwell-executions/captainAchab/125ed6dd-2cf6-417a-8456-32f4c307d094/call-bcftoolsNorm/inputs/-793930549/B00GMSH_leftalign.vcf; Date=Fri Jul 3 15:39:50 2020
##bcftools_normVersion=1.9+htslib-1.9
##reference=file:///home/guignardt/work-mobidic/nenufaar/refData/genome/hg19/hg19.fa
##INFO=ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"
##INFO=ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"
##INFO=ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"
##INFO=ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"
##INFO=ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"
##INFO=ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"
##INFO=ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"
##INFO=ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"
##INFO=ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"
##INFO=ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"
##INFO=ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"
##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"
##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"
##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"
##INFO=ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"
##INFO=ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"
##INFO=ID=POLYX,Number=1,Type=Integer,Description="Number of repeated bases around REF"
##INFO=ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"
##INFO=ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"
##INFO=ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"
##INFO=ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"
##INFO=ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR"
##INFO=ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR"
##INFO=ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR"
##INFO=ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR"
##INFO=ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR"
##INFO=ID=Approved_name.refGene,Number=.,Type=String,Description="Approved_name.refGene annotation provided by ANNOVAR"
##INFO=ID=Phenotypes.refGene,Number=.,Type=String,Description="Phenotypes.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper_rank.refGene,Number=.,Type=String,Description="oe_lof_upper_rank.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper_bin.refGene,Number=.,Type=String,Description="oe_lof_upper_bin.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof.refGene,Number=.,Type=String,Description="oe_lof.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_lower.refGene,Number=.,Type=String,Description="oe_lof_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_lof_upper.refGene,Number=.,Type=String,Description="oe_lof_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis.refGene,Number=.,Type=String,Description="oe_mis.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis_lower.refGene,Number=.,Type=String,Description="oe_mis_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_mis_upper.refGene,Number=.,Type=String,Description="oe_mis_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn.refGene,Number=.,Type=String,Description="oe_syn.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn_lower.refGene,Number=.,Type=String,Description="oe_syn_lower.refGene annotation provided by ANNOVAR"
##INFO=ID=oe_syn_upper.refGene,Number=.,Type=String,Description="oe_syn_upper.refGene annotation provided by ANNOVAR"
##INFO=ID=Function_description.refGene,Number=.,Type=String,Description="Function_description.refGene annotation provided by ANNOVAR"
##INFO=ID=Disease_description.refGene,Number=.,Type=String,Description="Disease_description.refGene annotation provided by ANNOVAR"
##INFO=ID=Tissue_specificity(Uniprot).refGene,Number=.,Type=String,Description="Tissue_specificity(Uniprot).refGene annotation provided by ANNOVAR"
##INFO=ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"
##INFO=ID=CLNDN,Number=.,Type=String,Description="CLNDN annotation provided by ANNOVAR"
##INFO=ID=CLNDISDB,Number=.,Type=String,Description="CLNDISDB annotation provided by ANNOVAR"
##INFO=ID=CLNREVSTAT,Number=.,Type=String,Description="CLNREVSTAT annotation provided by ANNOVAR"
##INFO=ID=CLNSIG,Number=.,Type=String,Description="CLNSIG annotation provided by ANNOVAR"
##INFO=ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"
##INFO=ID=SIFT_converted_rankscore,Number=.,Type=String,Description="SIFT_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_rankscore,Number=.,Type=String,Description="Polyphen2_HDIV_rankscore annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_rankscore,Number=.,Type=String,Description="Polyphen2_HVAR_rankscore annotation provided by ANNOVAR"
##INFO=ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"
##INFO=ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"
##INFO=ID=LRT_converted_rankscore,Number=.,Type=String,Description="LRT_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_converted_rankscore,Number=.,Type=String,Description="MutationTaster_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_score_rankscore,Number=.,Type=String,Description="MutationAssessor_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"
##INFO=ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"
##INFO=ID=FATHMM_converted_rankscore,Number=.,Type=String,Description="FATHMM_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_score,Number=.,Type=String,Description="PROVEAN_score annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_converted_rankscore,Number=.,Type=String,Description="PROVEAN_converted_rankscore annotation provided by ANNOVAR"
##INFO=ID=PROVEAN_pred,Number=.,Type=String,Description="PROVEAN_pred annotation provided by ANNOVAR"
##INFO=ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"
##INFO=ID=VEST3_rankscore,Number=.,Type=String,Description="VEST3_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_score,Number=.,Type=String,Description="MetaSVM_score annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_rankscore,Number=.,Type=String,Description="MetaSVM_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaSVM_pred,Number=.,Type=String,Description="MetaSVM_pred annotation provided by ANNOVAR"
##INFO=ID=MetaLR_score,Number=.,Type=String,Description="MetaLR_score annotation provided by ANNOVAR"
##INFO=ID=MetaLR_rankscore,Number=.,Type=String,Description="MetaLR_rankscore annotation provided by ANNOVAR"
##INFO=ID=MetaLR_pred,Number=.,Type=String,Description="MetaLR_pred annotation provided by ANNOVAR"
##INFO=ID=M-CAP_score,Number=.,Type=String,Description="M-CAP_score annotation provided by ANNOVAR"
##INFO=ID=M-CAP_rankscore,Number=.,Type=String,Description="M-CAP_rankscore annotation provided by ANNOVAR"
##INFO=ID=M-CAP_pred,Number=.,Type=String,Description="M-CAP_pred annotation provided by ANNOVAR"
##INFO=ID=REVEL_score,Number=.,Type=String,Description="REVEL_score annotation provided by ANNOVAR"
##INFO=ID=REVEL_rankscore,Number=.,Type=String,Description="REVEL_rankscore annotation provided by ANNOVAR"
##INFO=ID=MutPred_score,Number=.,Type=String,Description="MutPred_score annotation provided by ANNOVAR"
##INFO=ID=MutPred_rankscore,Number=.,Type=String,Description="MutPred_rankscore annotation provided by ANNOVAR"
##INFO=ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"
##INFO=ID=CADD_raw_rankscore,Number=.,Type=String,Description="CADD_raw_rankscore annotation provided by ANNOVAR"
##INFO=ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"
##INFO=ID=DANN_score,Number=.,Type=String,Description="DANN_score annotation provided by ANNOVAR"
##INFO=ID=DANN_rankscore,Number=.,Type=String,Description="DANN_rankscore annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_score,Number=.,Type=String,Description="fathmm-MKL_coding_score annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_rankscore,Number=.,Type=String,Description="fathmm-MKL_coding_rankscore annotation provided by ANNOVAR"
##INFO=ID=fathmm-MKL_coding_pred,Number=.,Type=String,Description="fathmm-MKL_coding_pred annotation provided by ANNOVAR"
##INFO=ID=Eigen_coding_or_noncoding,Number=.,Type=String,Description="Eigen_coding_or_noncoding annotation provided by ANNOVAR"
##INFO=ID=Eigen-raw,Number=.,Type=String,Description="Eigen-raw annotation provided by ANNOVAR"
##INFO=ID=Eigen-PC-raw,Number=.,Type=String,Description="Eigen-PC-raw annotation provided by ANNOVAR"
##INFO=ID=GenoCanyon_score,Number=.,Type=String,Description="GenoCanyon_score annotation provided by ANNOVAR"
##INFO=ID=GenoCanyon_score_rankscore,Number=.,Type=String,Description="GenoCanyon_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=integrated_fitCons_score,Number=.,Type=String,Description="integrated_fitCons_score annotation provided by ANNOVAR"
##INFO=ID=integrated_fitCons_score_rankscore,Number=.,Type=String,Description="integrated_fitCons_score_rankscore annotation provided by ANNOVAR"
##INFO=ID=integrated_confidence_value,Number=.,Type=String,Description="integrated_confidence_value annotation provided by ANNOVAR"
##INFO=ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"
##INFO=ID=GERP++_RS_rankscore,Number=.,Type=String,Description="GERP++_RS_rankscore annotation provided by ANNOVAR"
##INFO=ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"
##INFO=ID=phyloP100way_vertebrate_rankscore,Number=.,Type=String,Description="phyloP100way_vertebrate_rankscore annotation provided by ANNOVAR"
##INFO=ID=phyloP20way_mammalian,Number=.,Type=String,Description="phyloP20way_mammalian annotation provided by ANNOVAR"
##INFO=ID=phyloP20way_mammalian_rankscore,Number=.,Type=String,Description="phyloP20way_mammalian_rankscore annotation provided by ANNOVAR"
##INFO=ID=phastCons100way_vertebrate,Number=.,Type=String,Description="phastCons100way_vertebrate annotation provided by ANNOVAR"
##INFO=ID=phastCons100way_vertebrate_rankscore,Number=.,Type=String,Description="phastCons100way_vertebrate_rankscore annotation provided by ANNOVAR"
##INFO=ID=phastCons20way_mammalian,Number=.,Type=String,Description="phastCons20way_mammalian annotation provided by ANNOVAR"
##INFO=ID=phastCons20way_mammalian_rankscore,Number=.,Type=String,Description="phastCons20way_mammalian_rankscore annotation provided by ANNOVAR"
##INFO=ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"
##INFO=ID=SiPhy_29way_logOdds_rankscore,Number=.,Type=String,Description="SiPhy_29way_logOdds_rankscore annotation provided by ANNOVAR"
##INFO=ID=Interpro_domain,Number=.,Type=String,Description="Interpro_domain annotation provided by ANNOVAR"
##INFO=ID=GTEx_V6p_gene,Number=.,Type=String,Description="GTEx_V6p_gene annotation provided by ANNOVAR"
##INFO=ID=GTEx_V6p_tissue,Number=.,Type=String,Description="GTEx_V6p_tissue annotation provided by ANNOVAR"
##INFO=ID=dbscSNV_ADA_SCORE,Number=.,Type=String,Description="dbscSNV_ADA_SCORE annotation provided by ANNOVAR"
##INFO=ID=dbscSNV_RF_SCORE,Number=.,Type=String,Description="dbscSNV_RF_SCORE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_ALL,Number=.,Type=String,Description="gnomAD_exome_ALL annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_AFR,Number=.,Type=String,Description="gnomAD_exome_AFR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_AMR,Number=.,Type=String,Description="gnomAD_exome_AMR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_ASJ,Number=.,Type=String,Description="gnomAD_exome_ASJ annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_EAS,Number=.,Type=String,Description="gnomAD_exome_EAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_FIN,Number=.,Type=String,Description="gnomAD_exome_FIN annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_NFE,Number=.,Type=String,Description="gnomAD_exome_NFE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_OTH,Number=.,Type=String,Description="gnomAD_exome_OTH annotation provided by ANNOVAR"
##INFO=ID=gnomAD_exome_SAS,Number=.,Type=String,Description="gnomAD_exome_SAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_ALL,Number=.,Type=String,Description="gnomAD_genome_ALL annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_AFR,Number=.,Type=String,Description="gnomAD_genome_AFR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_AMR,Number=.,Type=String,Description="gnomAD_genome_AMR annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_ASJ,Number=.,Type=String,Description="gnomAD_genome_ASJ annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_EAS,Number=.,Type=String,Description="gnomAD_genome_EAS annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_FIN,Number=.,Type=String,Description="gnomAD_genome_FIN annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_NFE,Number=.,Type=String,Description="gnomAD_genome_NFE annotation provided by ANNOVAR"
##INFO=ID=gnomAD_genome_OTH,Number=.,Type=String,Description="gnomAD_genome_OTH annotation provided by ANNOVAR"
##INFO=ID=InterVar_automated,Number=.,Type=String,Description="InterVar_automated annotation provided by ANNOVAR"
##INFO=ID=PVS1,Number=.,Type=String,Description="PVS1 annotation provided by ANNOVAR"
##INFO=ID=PS1,Number=.,Type=String,Description="PS1 annotation provided by ANNOVAR"
##INFO=ID=PS2,Number=.,Type=String,Description="PS2 annotation provided by ANNOVAR"
##INFO=ID=PS3,Number=.,Type=String,Description="PS3 annotation provided by ANNOVAR"
##INFO=ID=PS4,Number=.,Type=String,Description="PS4 annotation provided by ANNOVAR"
##INFO=ID=PM1,Number=.,Type=String,Description="PM1 annotation provided by ANNOVAR"
##INFO=ID=PM2,Number=.,Type=String,Description="PM2 annotation provided by ANNOVAR"
##INFO=ID=PM3,Number=.,Type=String,Description="PM3 annotation provided by ANNOVAR"
##INFO=ID=PM4,Number=.,Type=String,Description="PM4 annotation provided by ANNOVAR"
##INFO=ID=PM5,Number=.,Type=String,Description="PM5 annotation provided by ANNOVAR"
##INFO=ID=PM6,Number=.,Type=String,Description="PM6 annotation provided by ANNOVAR"
##INFO=ID=PP1,Number=.,Type=String,Description="PP1 annotation provided by ANNOVAR"
##INFO=ID=PP2,Number=.,Type=String,Description="PP2 annotation provided by ANNOVAR"
##INFO=ID=PP3,Number=.,Type=String,Description="PP3 annotation provided by ANNOVAR"
##INFO=ID=PP4,Number=.,Type=String,Description="PP4 annotation provided by ANNOVAR"
##INFO=ID=PP5,Number=.,Type=String,Description="PP5 annotation provided by ANNOVAR"
##INFO=ID=BA1,Number=.,Type=String,Description="BA1 annotation provided by ANNOVAR"
##INFO=ID=BS1,Number=.,Type=String,Description="BS1 annotation provided by ANNOVAR"
##INFO=ID=BS2,Number=.,Type=String,Description="BS2 annotation provided by ANNOVAR"
##INFO=ID=BS3,Number=.,Type=String,Description="BS3 annotation provided by ANNOVAR"
##INFO=ID=BS4,Number=.,Type=String,Description="BS4 annotation provided by ANNOVAR"
##INFO=ID=BP1,Number=.,Type=String,Description="BP1 annotation provided by ANNOVAR"
##INFO=ID=BP2,Number=.,Type=String,Description="BP2 annotation provided by ANNOVAR"
##INFO=ID=BP3,Number=.,Type=String,Description="BP3 annotation provided by ANNOVAR"
##INFO=ID=BP4,Number=.,Type=String,Description="BP4 annotation provided by ANNOVAR"
##INFO=ID=BP5,Number=.,Type=String,Description="BP5 annotation provided by ANNOVAR"
##INFO=ID=BP6,Number=.,Type=String,Description="BP6 annotation provided by ANNOVAR"
##INFO=ID=BP7,Number=.,Type=String,Description="BP7 annotation provided by ANNOVAR"
##INFO=ID=spliceai_filtered,Number=.,Type=String,Description="spliceai_filtered annotation provided by ANNOVAR"
##INFO=ID=dpsi_max_tissue,Number=.,Type=String,Description="dpsi_max_tissue annotation provided by ANNOVAR"
##INFO=ID=dpsi_zscore,Number=.,Type=String,Description="dpsi_zscore annotation provided by ANNOVAR"
##INFO=ID=PopFreqMax,Number=.,Type=String,Description="PopFreqMax annotation provided by ANNOVAR"
##INFO=ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"
##INFO=ID=MPA_adjusted,Number=.,Type=String,Description="MPA_adjusted : normalize MPA missense score from 0 to 10"
##INFO=ID=MPA_available,Number=.,Type=String,Description="MPA_available : number of missense tools annotation available for this variant"
##INFO=ID=MPA_deleterious,Number=.,Type=String,Description="MPA_deleterious : number of missense tools that annotate this variant pathogenic"
##INFO=ID=MPA_final_score,Number=.,Type=String,Description="MPA_final_score : unique score that take into account curated database, biological assumptions, splicing predictions and the sum of various predictors for missense alterations. Annotations are made for exonic and splicing variants up to +300nt."
##INFO=ID=MPA_impact,Number=.,Type=String,Description="MPA_impact : pathogenic predictions (clinvar_pathogenicity, splice_impact, stop and frameshift_impact)"
##INFO=ID=MPA_ranking,Number=.,Type=String,Description="MPA_ranking : prioritize variants with ranks from 1 to 10"
##FORMAT=ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"
##FORMAT=ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"
##FORMAT=ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"
##FORMAT=ID=GT,Number=1,Type=String,Description="Genotype"
##FORMAT=ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"
##FILTER=ID=LowCoverage,Description="DP 20"
##FILTER=ID=LowMappingQuality,Description="MQ 10.00"
##FILTER=ID=LowQD,Description="QD 1.5"
##FILTER=ID=LowQual,Description="Low quality"
##FILTER=ID=PASS,Description="All filters passed"
##FILTER=ID=R8,Description="POLYX 7"
##FILTER=ID=StrandBias,Description="FS 60.000"
##contig=ID=chr1,length=249250621
##contig=ID=chr2,length=243199373
##contig=ID=chr3,length=198022430
##contig=ID=chr4,length=191154276
##contig=ID=chr5,length=180915260
##contig=ID=chr6,length=171115067
##contig=ID=chr7,length=159138663
##contig=ID=chr8,length=146364022
##contig=ID=chr9,length=141213431
##contig=ID=chr10,length=135534747
##contig=ID=chr11,length=135006516
##contig=ID=chr12,length=133851895
##contig=ID=chr13,length=115169878
##contig=ID=chr14,length=107349540
##contig=ID=chr15,length=102531392
##contig=ID=chr16,length=90354753
##contig=ID=chr17,length=81195210
##contig=ID=chr18,length=78077248
##contig=ID=chr19,length=59128983
##contig=ID=chr20,length=63025520
##contig=ID=chr21,length=48129895
##contig=ID=chr22,length=51304566
##contig=ID=chrX,length=155270560
##contig=ID=chrY,length=59373566
##contig=ID=chrM,length=16571
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B00GMSH B00GMSI B00GMSJ
</div>
<div id="ALL" class="tabcontent">
<table id='table' class="display compact" >
<thead><tr class="head"> <th class="rotate" ><div><span>MPA_ranking </span></div></th>
<th class="rotate" ><div><span>MPA_impact </span></div></th>
<th class="rotate" ><div><span>Phenolyzer </span></div></th>
<th class="rotate" ><div><span>Gene.refGene </span></div></th>
<th class="rotate" ><div><span>Phenotypes.refGene </span></div></th>
<th class="rotate" ><div><span>gnomAD_Genome </span></div></th>
<th class="rotate" ><div><span>gnomAD_Exome </span></div></th>
<th class="rotate" ><div><span>CLNSIG </span></div></th>
<th class="rotate" ><div><span>InterVar_automated </span></div></th>
<th class="rotate" ><div><span>SecondHit-CNV </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSH </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSI </span></div></th>
<th class="rotate" ><div><span>Genotype-B00GMSJ </span></div></th>
<th class="rotate" ><div><span>#CHROMPOSREFALT </span></div></th>
<th class="rotate" ><div><span>FILTER </span></div></th>
<th class="rotate" ><div><span>Case Depth </span></div></th>
<th class="rotate" ><div><span>Case AB </span></div></th>
</tr>
</thead>
<tbody>
<tr class="ALL" >
<td ><div class="tooltip">1<span class="tooltiptext tooltip-bottom">MPA_ranking = 3
MPA_final_score = 10
MPA_impact = splice_impact
MPA_adjusted = 0
MPA_available = 0
MPA_deleterious = 0
--- SPLICE ---
dbscSNV_ADA_SCORE = 0.9954
dbscSNV_RF_SCORE = 0.75
spliceai_filtered DS_AG=0.0000
spliceai_filtered DS_AL=0.0000
spliceai_filtered DS_DG=0.0008
spliceai_filtered DS_DL=0.4060
--- MISSENSE ---
LRT_pred = .
SIFT_pred = .
FATHMM_pred = .
MetaLR_pred = .
MetaSVM_pred = .
PROVEAN_pred = .
Polyphen2_HDIV_pred = .
Polyphen2_HVAR_pred = .
MutationTaster_pred = .
fathmm-MKL_coding_pred = .
</span></div> </td>
<td ><div class="tooltip"><a href="https://mobidetails.iurc.montp.inserm.fr/MD/vars/C1orf159"target="_blank" rel="noopener noreferrer">splice_impact</a><span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
.
AAChange.refGene:
.
GeneDetail.refGene:
NM_017891:exon2:UTR5
NM_001330306:exon3:UTR5
ID:
rs143221733
Func.refGene:
splicing
intronic
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#7FFF00"><div class="tooltip">C1orf159<span class="tooltiptext tooltip-bottom">LOEUF = 1.302
LOEUF_decile = 7.0
oe_lof = 0.69466
oe_lof_lower = 0.394
Missense_upper = 1.016
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">0.0053<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 0.0053
gnomAD_genome_AFR = 0.0014
gnomAD_genome_AMR = 0.0024
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0.0052
gnomAD_genome_NFE = 0.0084
gnomAD_genome_OTH = 0.0051
</span></div> </td>
<td ><div class="tooltip">0.0047<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 0.0047
gnomAD_exome_AFR = 0.0017
gnomAD_exome_AMR = 0.0017
gnomAD_exome_ASJ = 0.0041
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0.0091
gnomAD_exome_NFE = 0.0083
gnomAD_exome_OTH = 0.0049
gnomAD_exome_SAS = 0.0022
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td><div class="tooltip">.</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 2523.16
Genotype-B00GMSH - 0/1
DP = 96 AD = 52,44 AB = 0.458
Genotype-B00GMSI - 0/0
DP = 110 AD = 109,1 AB = 0.009
Genotype-B00GMSJ - 0/1
DP = 105 AD = 61,44 AB = 0.419
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td ><div class="tooltip"><a href="https://franklin.genoox.com/clinical-db/variant/snp/chr1-1027366-C-T-hg19"target="_blank" rel="noopener noreferrer">chr1-1027366-C-T</a></div> </td>
<td><div class="tooltip">PASS</div> </td>
<td><div class="tooltip">96</div> </td>
<td><div class="tooltip">0.458</div> </td>
</tr>
<tr class="ALL" >
<td ><div class="tooltip">2<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 10.0
MPA_impact = missense_impact
MPA_adjusted = 10.0
MPA_available = 10
MPA_deleterious = 10
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = D
MetaLR_pred = D
MetaSVM_pred = D
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td ><div class="tooltip"><a href="https://mobidetails.iurc.montp.inserm.fr/MD/vars/PLA2G2F"target="_blank" rel="noopener noreferrer">10_missense_impact</a><span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
PLA2G2F:NM_022819:exon3:c.G262A:p.G88S
PLA2G2F:NM_022819:exon3:c.262G>A:p.G88S
GeneDetail.refGene:
.
ID:
.
Func.refGene:
exonic
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#00FF00"><div class="tooltip">PLA2G2F<span class="tooltiptext tooltip-bottom">LOEUF = 1.817
LOEUF_decile = 9.0
oe_lof = 1.1229
oe_lof_lower = 0.651
Missense_upper = 1.237
Function Description:
FUNCTION:_May_play_a_role_in_lipid_mediator_production_in_inflammatory_conditions,_by_providing_arachidonic_acid_to_downstream_cyclooxygenases_and_lipoxygenases_(By_similarity)._Phospholipase_A2,_which_catalyzes_the_calcium_dependent_hydrolysis_of_the_2_acyl_groups_in_3_sn_phosphoglycerides_(PubMed:11112443)._Hydrolyzes_phosphatidylethanolamine_more_efficiently_than_phosphatidylcholine,_with_only_a_modest_preference_for_arachidonic_acid_versus_linoelic_acid_at_the_sn_2_position._Comparable_activity_toward_1_palmitoyl_2_oleoyl_phosphatidylserine_vesicles_to_that_toward_1_palmitoyl_2_oleoyl_phosphatidylglycerol_(By_similarity)._Hydrolyzes_phosphatidylglycerol_versus_phosphatidylcholine_with_a_15_fold_preference_(PubMed:11112443)._{ECO:0000250|UniProtKB:Q9QZT4,_ECO:0000269|PubMed:11112443}.
Tissue specificity:
TISSUE_SPECIFICITY:_Expressed_at_high_levels_in_placenta,_testis,_thymus_and_at_lower_levels_in_heart,_kidney,_liver_and_prostate_(PubMed:11112443)._Highly_expressed_in_rheumatoid_arthritic_tissues,_including_synovial_lining_cells_in_the_intima,_capillary_endothelial_cells_and_plasma_cells_(PubMed:11877435)._{ECO:0000269|PubMed:11112443,_ECO:0000269|PubMed:11877435}.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">3.233e-05<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 3.233e-05
gnomAD_genome_AFR = 0
gnomAD_genome_AMR = 0
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0
gnomAD_genome_NFE = 0
gnomAD_genome_OTH = 0.0010
</span></div> </td>
<td ><div class="tooltip">4.068e-06<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 4.068e-06
gnomAD_exome_AFR = 0
gnomAD_exome_AMR = 0
gnomAD_exome_ASJ = 0
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0
gnomAD_exome_NFE = 8.982e-06
gnomAD_exome_OTH = 0
gnomAD_exome_SAS = 0
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
PP3 = 1
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) sfit for conservation, GERP++_RS for evolutionary, splicing impact from dbNSFP
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 2455.16
Genotype-B00GMSH - 0/1
DP = 73 AD = 31,42 AB = 0.575
Genotype-B00GMSI - 0/0
DP = 59 AD = 59,0 AB = 0
Genotype-B00GMSJ - 0/1
DP = 82 AD = 43,39 AB = 0.475
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td ><div class="tooltip"><a href="https://franklin.genoox.com/clinical-db/variant/snp/chr1-20470031-G-A-hg19"target="_blank" rel="noopener noreferrer">chr1-20470031-G-A</a></div> </td>
<td><div class="tooltip">PASS</div> </td>
<td><div class="tooltip">73</div> </td>
<td><div class="tooltip">0.575</div> </td>
</tr>
<tr class="ALL OMIMREC" >
<td ><div class="tooltip">3<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 9.0
MPA_impact = missense_impact
MPA_adjusted = 9.0
MPA_available = 10
MPA_deleterious = 9
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = T
MetaLR_pred = D
MetaSVM_pred = D
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td ><div class="tooltip"><a href="https://mobidetails.iurc.montp.inserm.fr/MD/vars/H6PD"target="_blank" rel="noopener noreferrer">9_missense_impact</a><span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
H6PD:NM_001282587:exon5:c.C1802T:p.S601L
H6PD:NM_004285:exon5:c.C1769T:p.S590L
H6PD:NM_001282587:exon5:c.1802C>T:p.S601L
H6PD:NM_004285:exon5:c.1769C>T:p.S590L
GeneDetail.refGene:
.
ID:
.
Func.refGene:
exonic
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#FFFF00"><div class="tooltip">H6PD<span class="tooltiptext tooltip-bottom">LOEUF = 0.941
LOEUF_decile = 5.0
oe_lof = 0.6271399999999999
oe_lof_lower = 0.428
Missense_upper = 1.23
Function Description:
FUNCTION:_Bifunctional_enzyme_localized_in_the_lumen_of_the_endoplasmic_reticulum_that_catalyzes_the_first_two_steps_of_the_oxidative_branch_of_the_pentose_phosphate_pathway/shunt,_an_alternative_to_glycolysis_and_a_major_source_of_reducing_power_and_metabolic_intermediates_for_biosynthetic_processes_(By_similarity)._Has_a_hexose_6_phosphate_dehydrogenase_activity,_with_broad_substrate_specificity_compared_to_glucose_6_phosphate_1_dehydrogenase/G6PD,_and_catalyzes_the_first_step_of_the_pentose_phosphate_pathway_(PubMed:12858176,_PubMed:18628520,_PubMed:23132696)._In_addition,_acts_as_a_6_phosphogluconolactonase_and_catalyzes_the_second_step_of_the_pentose_phosphate_pathway_(By_similarity)._May_have_a_dehydrogenase_activity_for_alternative_substrates_including_glucosamine_6_phosphate_and_glucose_6_sulfate_(By_similarity)._The_main_function_of_this_enzyme_is_to_provide_reducing_equivalents_such_as_NADPH_to_maintain_the_adequate_levels_of_reductive_cofactors_in_the_oxidizing_environment_of_the_endoplasmic_reticulum_(PubMed:12858176,_PubMed:18628520,_PubMed:23132696)._By_producing_NADPH_that_is_needed_by_reductases_of_the_lumen_of_the_endoplasmic_reticulum_like_corticosteroid_11_beta_dehydrogenase_isozyme_1/HSD11B1,_indirectly_regulates_their_activity_(PubMed:18628520)._{ECO:0000250|UniProtKB:Q8CFX1,_ECO:0000269|PubMed:12858176,_ECO:0000269|PubMed:18628520,_ECO:0000269|PubMed:23132696}.
Tissue specificity:
TISSUE_SPECIFICITY:_Present_in_most_tissues_examined,_strongest_in_liver._{ECO:0000269|PubMed:10349511}.
</span></div> </td>
<td ><div class="tooltip">Cortisone_reductase_deficiency_1,_604931__3_,_Autosomal_recessive<span class="tooltiptext tooltip-bottom">Cortisone_reductase_deficiency_1,_604931__3_,_Autosomal_recessive
Disease_description.refGene:
DISEASE:_Cortisone_reductase_deficiency_1_(CORTRD1)_[MIM:604931]:_An_autosomal_recessive_error_of_cortisone_metabolism_characterized_by_a_failure_to_regenerate_cortisol_from_cortisone,_resulting_in_increased_cortisol_clearance,_activation_of_the_hypothalamic_pituitary_axis_and_ACTH_mediated_adrenal_androgen_excess._Clinical_features_include_hyperandrogenism_resulting_in_hirsutism,_oligo_amenorrhea,_and_infertility_in_females_and_premature_pseudopuberty_in_males._{ECO:0000269|PubMed:12858176,_ECO:0000269|PubMed:17974005,_ECO:0000269|PubMed:18628520,_ECO:0000269|PubMed:23132696}._Note=The_disease_is_caused_by_mutations_affecting_the_gene_represented_in_this_entry.
</span></div> </td>
<td ><div class="tooltip">3.233e-05<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 3.233e-05
gnomAD_genome_AFR = 0.0001
gnomAD_genome_AMR = 0
gnomAD_genome_ASJ = 0
gnomAD_genome_EAS = 0
gnomAD_genome_FIN = 0
gnomAD_genome_NFE = 0
gnomAD_genome_OTH = 0
</span></div> </td>
<td ><div class="tooltip">8.577e-06<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 8.577e-06
gnomAD_exome_AFR = 7.179e-05
gnomAD_exome_AMR = 0
gnomAD_exome_ASJ = 0
gnomAD_exome_EAS = 0
gnomAD_exome_FIN = 0
gnomAD_exome_NFE = 9.54e-06
gnomAD_exome_OTH = 0
gnomAD_exome_SAS = 0
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
PP3 = 1
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.) sfit for conservation, GERP++_RS for evolutionary, splicing impact from dbNSFP
PM2 = 1
Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 3859.16
Genotype-B00GMSH - 0/1
DP = 100 AD = 48,52 AB = 0.52
Genotype-B00GMSI - 0/1
DP = 143 AD = 71,72 AB = 0.503
Genotype-B00GMSJ - 0/0
DP = 137 AD = 137,0 AB = 0
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td ><div class="tooltip"><a href="https://franklin.genoox.com/clinical-db/variant/snp/chr1-9324321-C-T-hg19"target="_blank" rel="noopener noreferrer">chr1-9324321-C-T</a></div> </td>
<td><div class="tooltip">PASS</div> </td>
<td><div class="tooltip">100</div> </td>
<td><div class="tooltip">0.52</div> </td>
</tr>
<tr class="ALL" >
<td ><div class="tooltip">4<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 7.0
MPA_impact = missense_impact
MPA_adjusted = 7.0
MPA_available = 10
MPA_deleterious = 7
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered = .
--- MISSENSE ---
LRT_pred = D
SIFT_pred = D
FATHMM_pred = T
MetaLR_pred = T
MetaSVM_pred = T
PROVEAN_pred = D
Polyphen2_HDIV_pred = D
Polyphen2_HVAR_pred = D
MutationTaster_pred = D
fathmm-MKL_coding_pred = D
</span></div> </td>
<td ><div class="tooltip"><a href="https://mobidetails.iurc.montp.inserm.fr/MD/vars/EPHA8"target="_blank" rel="noopener noreferrer">7_missense_impact</a><span class="tooltiptext tooltip-bottom">ExonicFunc.refGene:
nonsynonymous_SNV
AAChange.refGene:
EPHA8:NM_020526:exon10:c.A1892G:p.E631G
EPHA8:NM_020526:exon10:c.1892A>G:p.E631G
GeneDetail.refGene:
.
ID:
.
Func.refGene:
exonic
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom"></span></div> </td>
<td style="background-color:#FF9900"><div class="tooltip">EPHA8<span class="tooltiptext tooltip-bottom">LOEUF = 0.712
LOEUF_decile = 3.0
oe_lof = 0.506
oe_lof_lower = 0.365
Missense_upper = 0.987
Function Description:
FUNCTION:_Receptor_tyrosine_kinase_which_binds_promiscuously_GPI_anchored_ephrin_A_family_ligands_residing_on_adjacent_cells,_leading_to_contact_dependent_bidirectional_signaling_into_neighboring_cells._The_signaling_pathway_downstream_of_the_receptor_is_referred_to_as_forward_signaling_while_the_signaling_pathway_downstream_of_the_ephrin_ligand_is_referred_to_as_reverse_signaling._The_GPI_anchored_ephrin_A_EFNA2,_EFNA3,_and_EFNA5_are_able_to_activate_EPHA8_through_phosphorylation._With_EFNA5_may_regulate_integrin_mediated_cell_adhesion_and_migration_on_fibronectin_substrate_but_also_neurite_outgrowth._During_development_of_the_nervous_system_plays_also_a_role_in_axon_guidance._Downstream_effectors_of_the_EPHA8_signaling_pathway_include_FYN_which_promotes_cell_adhesion_upon_activation_by_EPHA8_and_the_MAP_kinases_in_the_stimulation_of_neurite_outgrowth_(By_similarity)._{ECO:0000250}.;FUNCTION:_Receptor_tyrosine_kinase_which_binds_promiscuously_GPI_anchored_ephrin_A_family_ligands_residing_on_adjacent_cells,_leading_to_contact_dependent_bidirectional_signaling_into_neighboring_cells._The_signaling_pathway_downstream_of_the_receptor_is_referred_to_as_forward_signaling_while_the_signaling_pathway_downstream_of_the_ephrin_ligand_is_referred_to_as_reverse_signaling._The_GPI_anchored_ephrin_A_EFNA2,_EFNA3,_and_EFNA5_are_able_to_activate_EPHA8_through_phosphorylation._With_EFNA5_may_regulate_integrin_mediated_cell_adhesion_and_migration_on_fibronectin_substrate_but_also_neurite_outgrowth._During_development_of_the_nervous_system_plays_also_a_role_in_axon_guidance._Downstream_effectors_of_the_EPHA8_signaling_pathway_include_FYN_which_promotes_cell_adhesion_upon_activation_by_EPHA8_and_the_MAP_kinases_in_the_stimulation_of_neurite_outgrowth_(By_similarity)._{ECO:0000250}.
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">.
Disease_description.refGene:
.
</span></div> </td>
<td ><div class="tooltip">0<span class="tooltiptext tooltip-bottom">gnomAD_genome_ALL = 0
gnomAD_genome_AFR = .
gnomAD_genome_AMR = .
gnomAD_genome_ASJ = .
gnomAD_genome_EAS = .
gnomAD_genome_FIN = .
gnomAD_genome_NFE = .
gnomAD_genome_OTH = .
</span></div> </td>
<td ><div class="tooltip">0<span class="tooltiptext tooltip-bottom">gnomAD_exome_ALL = 0
gnomAD_exome_AFR = .
gnomAD_exome_AMR = .
gnomAD_exome_ASJ = .
gnomAD_exome_EAS = .
gnomAD_exome_FIN = .
gnomAD_exome_NFE = .
gnomAD_exome_OTH = .
gnomAD_exome_SAS = .
</span></div> </td>
<td ><div class="tooltip">.<span class="tooltiptext tooltip-bottom">CLNREVSTAT:
.
CLNDN:
.
CLNALLELEID:
.
CLNDISDB:
.
</span></div> </td>
<td ><div class="tooltip">Uncertain_significance<span class="tooltiptext tooltip-bottom">PM1 = 1
Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
PM2 = 1
Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
</span></div> </td>
<td><div class="tooltip">.</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1<span class="tooltiptext tooltip-bottom">CALLER = GATK QUALITY = 3067.16
Genotype-B00GMSH - 0/1
DP = 105 AD = 53,52 AB = 0.495
Genotype-B00GMSI - 0/0
DP = 138 AD = 138,0 AB = 0
Genotype-B00GMSJ - 0/1
DP = 148 AD = 81,67 AB = 0.452
</span></div> </td>
<td style="background-color:inherit"><div class="tooltip">0/0</div> </td>
<td style="background-color:inherit"><div class="tooltip">0/1</div> </td>
<td ><div class="tooltip"><a href="https://franklin.genoox.com/clinical-db/variant/snp/chr1-22923931-A-G-hg19"target="_blank" rel="noopener noreferrer">chr1-22923931-A-G</a></div> </td>
<td><div class="tooltip">PASS</div> </td>
<td><div class="tooltip">105</div> </td>
<td><div class="tooltip">0.495</div> </td>
</tr>
<tr class="ALL" >
<td ><div class="tooltip">5<span class="tooltiptext tooltip-bottom">MPA_ranking = 5
MPA_final_score = 7.0
MPA_impact = missense_impact,splice_impact
MPA_adjusted = 7.0
MPA_available = 10
MPA_deleterious = 7
--- SPLICE ---
dbscSNV_ADA_SCORE = .
dbscSNV_RF_SCORE = .
spliceai_filtered DS_AG=0.3887
spliceai_filtered DS_AL=0.0000
spliceai_filtered DS_DG=0.0000