##fileformat=VCFv4.1
##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)">
##FILTER=<ID=LowCoverage,Description="DP < 5">
##FILTER=<ID=LowQD,Description="QD < 1.5">
##FILTER=<ID=LowQual,Description="QUAL > 30.0 && QUAL <	50.0">
##FILTER=<ID=SnpCluster,Description="SNPs found	in clusters">
##FILTER=<ID=StrandBias,Description="FS	> 60.0">
##FILTER=<ID=VeryLowQual,Description="QUAL < 30.0">
##FORMAT=<ID=AD,Number=.,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">
##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=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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##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=MQ0,Number=1,Type=Integer,Description="Total	Mapping	Quality	Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat	unit is	repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from	Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[aln.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[target_gatk.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0	performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT	remove_program_records=false keep_program_records=false	unsafe=null 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 logging_level=INFO	log_to_file=null help=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25	indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name=	source=UNBOUND)	reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null exactcallslog=null dbsnp=(RodBinding	name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null	annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null	excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genome.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 enable_experimental_downsampling=false	baq=OFF	baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null	quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null	help=false variant=(RodBinding name=variant source=variants_raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub	no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub	bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[MQ0 >= 4 && ((MQ0	/ (1.0 * DP)) >	0.1), DP < 5, QUAL < 30.0, QUAL	> 30.0 && QUAL < 50.0, QD < 1.5, FS > 60.0] filterName=[HARD_TO_VALIDATE, LowCoverage, VeryLowQual, LowQual, LowQD, StrandBias]	genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3	clusterWindowSize=10 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false"
##contig=<ID=chr10,length=130694993>
##contig=<ID=chr11,length=122082543>
##contig=<ID=chr12,length=120129022>
##contig=<ID=chr13,length=120421639>
##contig=<ID=chr14,length=124902244>
##contig=<ID=chr15,length=104043685>
##contig=<ID=chr16,length=98207768>
##contig=<ID=chr17,length=94987271>
##contig=<ID=chr18,length=90702639>
##contig=<ID=chr19,length=61431566>
##contig=<ID=chr1,length=195471971>
##contig=<ID=chr2,length=182113224>
##contig=<ID=chr3,length=160039680>
##contig=<ID=chr4,length=156508116>
##contig=<ID=chr5,length=151834684>
##contig=<ID=chr6,length=149736546>
##contig=<ID=chr7,length=145441459>
##contig=<ID=chr8,length=129401213>
##contig=<ID=chr9,length=124595110>
##contig=<ID=chrM,length=16299>
##contig=<ID=chrX,length=171031299>
##contig=<ID=chrY,length=91744698>
##reference=file://genome.fa
##source_20130924.1=vcf-annotate(r797) -a dbSNP.mm10.tab.gz -c	CHROM,FROM,TO,ID
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	mouse1
chr11	3131821	rs13467127;rs249224453	A	G	2456.77	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.299;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=6.6626;MLEAC=2;MLEAF=1.00;MQ=52.35;MQ0=5;MQRankSum=-0.495;QD=25.33;ReadPosRankSum=1.673	GT:AD:DP:GQ:PL	1/1:2,95:91:99:2485,246,0
chr11	3131904	.	C	A	2586.77	HARD_TO_VALIDATE	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.667;DP=119;Dels=0.00;FS=3.218;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=12;MQRankSum=-1.473;QD=21.74;ReadPosRankSum=0.890	GT:AD:DP:GQ:PL	1/1:1,118:113:99:2615,291,0
chr11	3134297	rs264252937	G	A	712.77	SnpCluster	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.744;DP=87;Dels=0.00;FS=11.620;HaplotypeScore=1.8835;MLEAC=2;MLEAF=1.00;MQ=24.47;MQ0=7;MQRankSum=-4.064;QD=8.19;ReadPosRankSum=-1.196	GT:AD:DP:GQ:PL	1/1:6,81:79:32:741,32,0
chr11	3134337	.	G	A	438.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.322;DP=78;Dels=0.00;FS=7.469;HaplotypeScore=12.0245;MLEAC=1;MLEAF=0.500;MQ=33.40;MQ0=7;MQRankSum=-1.304;QD=5.63;ReadPosRankSum=1.737	GT:AD:DP:GQ:PL	0/1:34,44:72:99:467,0,301
chr11	3135671	.	C	T	909.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500;DP=63;Dels=0.00;FS=1.327;HaplotypeScore=1.8907;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-0.524;QD=14.44;ReadPosRankSum=0.317	GT:AD:DP:GQ:PL	0/1:20,43:57:99:938,0,377
chr11	3140099	.	C	A	824.77	SnpCluster	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.570;DP=80;Dels=0.00;FS=1.980;HaplotypeScore=18.6442;MLEAC=1;MLEAF=0.500;MQ=50.15;MQ0=0;MQRankSum=0.769;QD=10.31;ReadPosRankSum=0.223	GT:AD:DP:GQ:PL	0/1:33,45:70:99:853,0,614
chr11	3142297	.	C	A	963.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-10.342;DP=159;Dels=0.00;FS=1.278;HaplotypeScore=3.0933;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.584;QD=6.06;ReadPosRankSum=-0.539	GT:AD:DP:GQ:PL	0/1:97,62:145:99:992,0,2251
chr1	78180411	.	A	C	963.77	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-10.342;DP=159;Dels=0.00;FS=1.278;HaplotypeScore=3.0933;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.584;QD=6.06;ReadPosRankSum=-0.539	GT:AD:DP:GQ:PL	0/1:97,62:145:99:992,0,2251
chrX	53690930	.	T	C	74.10	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=0.736;QD=12.35;ReadPosRankSum=-0.736	GT:AD:DP:GQ:PL	0/1:1,5:6:11:102,0,11
chrX	53691000	rs250225376;rs226941554	G	C	47.81	LowCoverage;LowQual;SnpCluster	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-0.727;QD=11.95;ReadPosRankSum=0.727	GT:AD:DP:GQ:PL	0/1:1,3:4:20:76,0,20
chrX	53691001	.	G	C	45.85	LowCoverage;LowQual;SnpCluster	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=11.46;ReadPosRankSum=0.727	GT:AD:DP:GQ:PL	0/1:1,3:4:17:74,0,17
chrX	53691003	.	G	A	44.84	LowCoverage;LowQual;SnpCluster	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=11.21;ReadPosRankSum=0.727	GT:AD:DP:GQ:PL	0/1:1,3:4:18:73,0,18