diff test-data/01_1787_FL_Zoo_Jaguar.vcf @ 8:e54b96acea98 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
author iuc
date Tue, 16 Nov 2021 08:29:11 +0000
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/01_1787_FL_Zoo_Jaguar.vcf	Tue Nov 16 08:29:11 2021 +0000
@@ -0,0 +1,3765 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=LowQual,Description="Low quality">
+##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">
+##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Fri Dec 22 16:41:19 CST 2017",Epoch=1513982479531,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/01-1787-quality.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/NC_002945v4.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 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=/scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/01-1787-hapall.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE 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=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 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=true numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 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=true 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">
+##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=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=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">
+##contig=<ID=NC_002945.4,length=4349904>
+##reference=file:///scratch/analysis_staging/a_script/bovis_reanalysis_af2122_2017-12-14/2001-2008/01-1787/NC_002945v4.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	01-1787
+NC_002945.4	1057	.	A	G	10912.77	.	AC=2;AF=1.00;AN=2;DP=397;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.56;SOR=0.703	GT:AD:DP:GQ:PL	1/1:0,396:396:99:10941,1177,0
+NC_002945.4	8741	.	T	C	8362.77	.	AC=2;AF=1.00;AN=2;DP=250;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.45;SOR=1.392	GT:AD:DP:GQ:PL	1/1:0,250:250:99:8391,748,0
+NC_002945.4	14487	.	C	G	6175.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.669;ClippingRankSum=0.000;DP=165;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.88;ReadPosRankSum=-0.324;SOR=4.804	GT:AD:DP:GQ:PL	1/1:1,159:160:99:6204,468,0
+NC_002945.4	33788	.	A	G	7640.77	.	AC=2;AF=1.00;AN=2;DP=180;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=4.828	GT:AD:DP:GQ:PL	1/1:0,180:180:99:7669,542,0
+NC_002945.4	41437	.	T	C	10083.77	.	AC=2;AF=1.00;AN=2;DP=342;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.870	GT:AD:DP:GQ:PL	1/1:0,342:342:99:10112,1020,0
+NC_002945.4	57197	.	G	C	3714.77	.	AC=2;AF=1.00;AN=2;DP=120;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.21;SOR=3.809	GT:AD:DP:GQ:PL	1/1:0,105:105:99:3743,315,0
+NC_002945.4	67098	.	G	A	7793.77	.	AC=2;AF=1.00;AN=2;DP=260;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.09;SOR=0.867	GT:AD:DP:GQ:PL	1/1:0,259:259:99:7822,775,0
+NC_002945.4	69913	.	T	C	10036.77	.	AC=2;AF=1.00;AN=2;DP=321;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.27;SOR=0.725	GT:AD:DP:GQ:PL	1/1:0,321:321:99:10065,956,0
+NC_002945.4	103928	.	G	C	4649.77	.	AC=2;AF=1.00;AN=2;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.64;QD=27.17;SOR=2.573	GT:AD:DP:GQ:PL	1/1:0,110:110:99:4678,331,0
+NC_002945.4	103931	.	G	C	4505.77	.	AC=2;AF=1.00;AN=2;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.18;QD=26.01;SOR=2.509	GT:AD:DP:GQ:PL	1/1:0,107:107:99:4534,321,0
+NC_002945.4	104264	.	A	G	241.80	.	AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.54;QD=34.54;SOR=4.174	GT:AD:DP:GQ:PL	1/1:0,7:7:21:270,21,0
+NC_002945.4	119328	.	G	T	12064.77	.	AC=2;AF=1.00;AN=2;DP=423;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.52;SOR=0.736	GT:AD:DP:GQ:PL	1/1:0,423:423:99:12093,1260,0
+NC_002945.4	127447	.	G	C	6051.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.843;ClippingRankSum=0.000;DP=196;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.52;ReadPosRankSum=-0.504;SOR=0.572	GT:AD:DP:GQ:PL	1/1:1,191:192:99:6080,562,0
+NC_002945.4	130237	.	T	C	8833.77	.	AC=2;AF=1.00;AN=2;DP=293;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.15;SOR=1.012	GT:AD:DP:GQ:PL	1/1:0,293:293:99:8862,869,0
+NC_002945.4	159370	.	A	G	6799.77	.	AC=2;AF=1.00;AN=2;DP=217;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.34;SOR=0.779	GT:AD:DP:GQ:PL	1/1:0,217:217:99:6828,648,0
+NC_002945.4	160535	.	T	C	8515.77	.	AC=2;AF=1.00;AN=2;DP=279;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=1.329	GT:AD:DP:GQ:PL	1/1:0,278:278:99:8544,826,0
+NC_002945.4	165799	.	G	A	8624.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.926;ClippingRankSum=0.000;DP=307;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.19;ReadPosRankSum=1.442;SOR=0.272	GT:AD:DP:GQ:PL	1/1:1,305:306:99:8653,897,0
+NC_002945.4	166696	.	A	G	6491.77	.	AC=2;AF=1.00;AN=2;DP=214;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.77;SOR=1.079	GT:AD:DP:GQ:PL	1/1:0,211:211:99:6520,627,0
+NC_002945.4	180444	.	T	C	8771.77	.	AC=2;AF=1.00;AN=2;DP=315;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.94;SOR=1.168	GT:AD:DP:GQ:PL	1/1:0,314:314:99:8800,931,0
+NC_002945.4	182704	.	G	A	7366.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.976;ClippingRankSum=0.000;DP=272;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.49;ReadPosRankSum=1.545;SOR=0.382	GT:AD:DP:GQ:PL	1/1:3,265:268:99:7395,761,0
+NC_002945.4	185429	.	T	C	6597.77	.	AC=2;AF=1.00;AN=2;DP=187;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.02;SOR=2.760	GT:AD:DP:GQ:PL	1/1:0,187:187:99:6626,561,0
+NC_002945.4	228660	.	C	T	6295.77	.	AC=2;AF=1.00;AN=2;DP=232;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.49;SOR=0.892	GT:AD:DP:GQ:PL	1/1:0,229:229:99:6324,681,0
+NC_002945.4	232188	.	G	C	4879.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.654;ClippingRankSum=0.000;DP=179;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.94;ReadPosRankSum=1.419;SOR=0.712	GT:AD:DP:GQ:PL	1/1:1,162:163:99:4908,474,0
+NC_002945.4	246207	.	C	T	8706.77	.	AC=2;AF=1.00;AN=2;DP=298;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.22;SOR=0.806	GT:AD:DP:GQ:PL	1/1:0,298:298:99:8735,889,0
+NC_002945.4	255465	.	A	G	9237.77	.	AC=2;AF=1.00;AN=2;DP=284;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.53;SOR=0.875	GT:AD:DP:GQ:PL	1/1:0,284:284:99:9266,848,0
+NC_002945.4	295519	.	T	C	9658.77	.	AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.36;SOR=0.719	GT:AD:DP:GQ:PL	1/1:0,308:308:99:9687,920,0
+NC_002945.4	306689	.	N	.	.	.	.	GT	./.
+NC_002945.4	306690	.	N	.	.	.	.	GT	./.
+NC_002945.4	306691	.	N	.	.	.	.	GT	./.
+NC_002945.4	306692	.	N	.	.	.	.	GT	./.
+NC_002945.4	306693	.	N	.	.	.	.	GT	./.
+NC_002945.4	306694	.	N	.	.	.	.	GT	./.
+NC_002945.4	306695	.	N	.	.	.	.	GT	./.
+NC_002945.4	306696	.	N	.	.	.	.	GT	./.
+NC_002945.4	306697	.	N	.	.	.	.	GT	./.
+NC_002945.4	306698	.	N	.	.	.	.	GT	./.
+NC_002945.4	306699	.	N	.	.	.	.	GT	./.
+NC_002945.4	306700	.	N	.	.	.	.	GT	./.
+NC_002945.4	306701	.	N	.	.	.	.	GT	./.
+NC_002945.4	306702	.	N	.	.	.	.	GT	./.
+NC_002945.4	306703	.	N	.	.	.	.	GT	./.
+NC_002945.4	306704	.	N	.	.	.	.	GT	./.
+NC_002945.4	306705	.	N	.	.	.	.	GT	./.
+NC_002945.4	306706	.	N	.	.	.	.	GT	./.
+NC_002945.4	306707	.	N	.	.	.	.	GT	./.
+NC_002945.4	306708	.	N	.	.	.	.	GT	./.
+NC_002945.4	306709	.	N	.	.	.	.	GT	./.
+NC_002945.4	324581	.	G	A	8321.77	.	AC=2;AF=1.00;AN=2;DP=280;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.72;SOR=0.752	GT:AD:DP:GQ:PL	1/1:0,280:280:99:8350,837,0
+NC_002945.4	333332	.	N	.	.	.	.	GT	./.
+NC_002945.4	333333	.	N	.	.	.	.	GT	./.
+NC_002945.4	333334	.	N	.	.	.	.	GT	./.
+NC_002945.4	333335	.	N	.	.	.	.	GT	./.
+NC_002945.4	333336	.	N	.	.	.	.	GT	./.
+NC_002945.4	333337	.	N	.	.	.	.	GT	./.
+NC_002945.4	333338	.	N	.	.	.	.	GT	./.
+NC_002945.4	333342	.	N	.	.	.	.	GT	./.
+NC_002945.4	333343	.	N	.	.	.	.	GT	./.
+NC_002945.4	333344	.	N	.	.	.	.	GT	./.
+NC_002945.4	333345	.	N	.	.	.	.	GT	./.
+NC_002945.4	333346	.	N	.	.	.	.	GT	./.
+NC_002945.4	333347	.	N	.	.	.	.	GT	./.
+NC_002945.4	333363	.	N	.	.	.	.	GT	./.
+NC_002945.4	333364	.	N	.	.	.	.	GT	./.
+NC_002945.4	333365	.	N	.	.	.	.	GT	./.
+NC_002945.4	333366	.	N	.	.	.	.	GT	./.
+NC_002945.4	333367	.	N	.	.	.	.	GT	./.
+NC_002945.4	333368	.	N	.	.	.	.	GT	./.
+NC_002945.4	333369	.	N	.	.	.	.	GT	./.
+NC_002945.4	333370	.	N	.	.	.	.	GT	./.
+NC_002945.4	333371	.	N	.	.	.	.	GT	./.
+NC_002945.4	333372	.	N	.	.	.	.	GT	./.
+NC_002945.4	333373	.	N	.	.	.	.	GT	./.
+NC_002945.4	333374	.	N	.	.	.	.	GT	./.
+NC_002945.4	333375	.	N	.	.	.	.	GT	./.
+NC_002945.4	333376	.	N	.	.	.	.	GT	./.
+NC_002945.4	333377	.	N	.	.	.	.	GT	./.
+NC_002945.4	333378	.	N	.	.	.	.	GT	./.
+NC_002945.4	333379	.	N	.	.	.	.	GT	./.
+NC_002945.4	333380	.	N	.	.	.	.	GT	./.
+NC_002945.4	333381	.	N	.	.	.	.	GT	./.
+NC_002945.4	333382	.	N	.	.	.	.	GT	./.
+NC_002945.4	333383	.	N	.	.	.	.	GT	./.
+NC_002945.4	333384	.	N	.	.	.	.	GT	./.
+NC_002945.4	333385	.	N	.	.	.	.	GT	./.
+NC_002945.4	333386	.	N	.	.	.	.	GT	./.
+NC_002945.4	333387	.	N	.	.	.	.	GT	./.
+NC_002945.4	333388	.	N	.	.	.	.	GT	./.
+NC_002945.4	333389	.	N	.	.	.	.	GT	./.
+NC_002945.4	333390	.	N	.	.	.	.	GT	./.
+NC_002945.4	333391	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2412437	.	G	A	5042.77	.	AC=2;AF=1.00;AN=2;DP=182;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.86;SOR=0.871	GT:AD:DP:GQ:PL	1/1:0,181:181:99:5071,537,0
+NC_002945.4	2418267	.	G	A	6239.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.771;ClippingRankSum=0.000;DP=214;ExcessHet=3.0103;FS=3.200;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.57;ReadPosRankSum=1.035;SOR=0.377	GT:AD:DP:GQ:PL	1/1:1,210:211:99:6268,616,0
+NC_002945.4	2422964	.	G	A	966.77	.	AC=2;AF=1.00;AN=2;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.83;QD=34.53;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,28:28:84:995,84,0
+NC_002945.4	2423049	.	T	G	896.77	.	AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.65;QD=32.55;SOR=1.893	GT:AD:DP:GQ:PL	1/1:0,25:25:75:925,75,0
+NC_002945.4	2425939	.	G	A	7090.77	.	AC=2;AF=1.00;AN=2;DP=247;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.06;SOR=0.726	GT:AD:DP:GQ:PL	1/1:0,244:244:99:7119,726,0
+NC_002945.4	2426072	.	G	A	7305.77	.	AC=2;AF=1.00;AN=2;DP=264;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.88;SOR=0.772	GT:AD:DP:GQ:PL	1/1:0,262:262:99:7334,770,0
+NC_002945.4	2458252	.	C	T	9192.77	.	AC=2;AF=1.00;AN=2;DP=318;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.91;SOR=0.929	GT:AD:DP:GQ:PL	1/1:0,318:318:99:9221,948,0
+NC_002945.4	2479007	.	C	T	8049.77	.	AC=2;AF=1.00;AN=2;DP=279;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.06;SOR=0.760	GT:AD:DP:GQ:PL	1/1:0,277:277:99:8078,826,0
+NC_002945.4	2497022	.	C	G	10187.77	.	AC=2;AF=1.00;AN=2;DP=322;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.64;SOR=1.068	GT:AD:DP:GQ:PL	1/1:0,322:322:99:10216,960,0
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+NC_002945.4	2508626	.	G	T	7842.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.633;ClippingRankSum=0.000;DP=276;ExcessHet=3.0103;FS=7.758;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.26;ReadPosRankSum=-0.424;SOR=0.806	GT:AD:DP:GQ:PL	1/1:2,266:268:99:7871,778,0
+NC_002945.4	2512809	.	A	C	8540.77	.	AC=2;AF=1.00;AN=2;DP=282;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.29;SOR=0.980	GT:AD:DP:GQ:PL	1/1:0,282:282:99:8569,840,0
+NC_002945.4	2513801	.	C	A	4793.77	.	AC=2;AF=1.00;AN=2;DP=169;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.05;SOR=1.638	GT:AD:DP:GQ:PL	1/1:0,165:165:99:4822,487,0
+NC_002945.4	2515471	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2528517	.	T	C	9471.77	.	AC=2;AF=1.00;AN=2;DP=314;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.16;SOR=0.857	GT:AD:DP:GQ:PL	1/1:0,314:314:99:9500,935,0
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+NC_002945.4	2532958	.	G	A	6695.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.925;ClippingRankSum=0.000;DP=245;ExcessHet=3.0103;FS=11.724;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.67;ReadPosRankSum=-0.927;SOR=0.818	GT:AD:DP:GQ:PL	1/1:3,239:242:99:6724,681,0
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+NC_002945.4	2665769	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665770	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665771	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665773	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665774	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665775	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665776	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665783	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665787	.	N	.	.	.	.	GT	./.
+NC_002945.4	2665788	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665791	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665796	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2665804	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2755931	.	T	G	6960.77	.	AC=2;AF=1.00;AN=2;DP=212;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.47;SOR=1.509	GT:AD:DP:GQ:PL	1/1:0,208:208:99:6989,621,0
+NC_002945.4	2773444	.	G	A	63.28	.	AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.09;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:91,9,0
+NC_002945.4	2776121	.	N	.	.	.	.	GT	./.
+NC_002945.4	2776122	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2776124	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2776126	.	N	.	.	.	.	GT	./.
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+NC_002945.4	2998136	.	A	C	70.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.020;ClippingRankSum=0.000;DP=259;ExcessHet=3.0103;FS=444.660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=0.29;ReadPosRankSum=-11.131;SOR=8.553	GT:AD:DP:GQ:PL	0/1:175,71:246:99:99,0,3117
+NC_002945.4	3018593	.	G	T	7893.77	.	AC=2;AF=1.00;AN=2;DP=264;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.01;SOR=0.780	GT:AD:DP:GQ:PL	1/1:0,263:263:99:7922,787,0
+NC_002945.4	3036490	.	C	G	5254.77	.	AC=2;AF=1.00;AN=2;DP=165;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.85;SOR=0.834	GT:AD:DP:GQ:PL	1/1:0,165:165:99:5283,495,0
+NC_002945.4	3037620	.	C	G	7175.77	.	AC=2;AF=1.00;AN=2;DP=219;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.77;SOR=1.063	GT:AD:DP:GQ:PL	1/1:0,219:219:99:7204,655,0
+NC_002945.4	3040820	.	A	G	6881.77	.	AC=2;AF=1.00;AN=2;DP=204;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.73;SOR=0.753	GT:AD:DP:GQ:PL	1/1:0,204:204:99:6910,612,0
+NC_002945.4	3042914	.	T	A	8876.77	.	AC=2;AF=1.00;AN=2;DP=307;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.01;SOR=1.005	GT:AD:DP:GQ:PL	1/1:0,306:306:99:8905,910,0
+NC_002945.4	3047601	.	A	C	10229.77	.	AC=2;AF=1.00;AN=2;DP=331;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.91;SOR=0.971	GT:AD:DP:GQ:PL	1/1:0,331:331:99:10258,991,0
+NC_002945.4	3053649	.	G	A	7805.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=3.166;ClippingRankSum=0.000;DP=280;ExcessHet=3.0103;FS=10.058;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.08;ReadPosRankSum=1.447;SOR=0.377	GT:AD:DP:GQ:PL	1/1:3,275:278:99:7834,791,0
+NC_002945.4	3063074	.	A	G	9607.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.897;ClippingRankSum=0.000;DP=329;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.20;ReadPosRankSum=-0.757;SOR=0.420	GT:AD:DP:GQ:PL	1/1:1,328:329:99:9636,938,0
+NC_002945.4	3065929	.	A	C	5091.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.664;ClippingRankSum=0.000;DP=168;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.31;ReadPosRankSum=-0.668;SOR=0.331	GT:AD:DP:GQ:PL	1/1:1,167:168:99:5120,490,0
+NC_002945.4	3068041	.	A	G	5080.77	.	AC=2;AF=1.00;AN=2;DP=172;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.71;SOR=0.829	GT:AD:DP:GQ:PL	1/1:0,171:171:99:5109,509,0
+NC_002945.4	3070642	.	C	T	3071.77	.	AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.79;SOR=4.332	GT:AD:DP:GQ:PL	1/1:0,85:85:99:3100,254,0
+NC_002945.4	3080843	.	T	C	6017.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.408;ClippingRankSum=0.000;DP=232;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQRankSum=2.869;QD=26.28;ReadPosRankSum=2.094;SOR=0.739	GT:AD:DP:GQ:PL	1/1:8,221:229:99:6046,424,0
+NC_002945.4	3092170	.	G	A	9169.77	.	AC=2;AF=1.00;AN=2;DP=328;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.21;SOR=0.931	GT:AD:DP:GQ:PL	1/1:0,325:325:99:9198,966,0
+NC_002945.4	3098932	.	T	C	5776.77	.	AC=2;AF=1.00;AN=2;DP=178;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.45;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,178:178:99:5805,532,0
+NC_002945.4	3100639	.	G	C	4674.77	.	AC=2;AF=1.00;AN=2;DP=161;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.97;SOR=2.098	GT:AD:DP:GQ:PL	1/1:0,156:156:99:4703,459,0
+NC_002945.4	3103354	.	T	C	6427.77	.	AC=2;AF=1.00;AN=2;DP=203;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.46;SOR=1.746	GT:AD:DP:GQ:PL	1/1:0,198:198:99:6456,591,0
+NC_002945.4	3137471	.	A	G	7675.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.956;ClippingRankSum=0.000;DP=246;ExcessHet=3.0103;FS=3.136;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.33;ReadPosRankSum=-0.498;SOR=0.329	GT:AD:DP:GQ:PL	1/1:1,244:245:99:7704,723,0
+NC_002945.4	3140342	.	G	T	8580.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.979;ClippingRankSum=0.000;DP=307;ExcessHet=3.0103;FS=3.067;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=28.04;ReadPosRankSum=2.826;SOR=0.276	GT:AD:DP:GQ:PL	1/1:1,305:306:99:8609,898,0
+NC_002945.4	3147547	.	G	A	6453.77	.	AC=2;AF=1.00;AN=2;DP=241;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.12;SOR=0.817	GT:AD:DP:GQ:PL	1/1:0,238:238:99:6482,705,0
+NC_002945.4	3154140	.	T	C	10114.77	.	AC=2;AF=1.00;AN=2;DP=332;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.47;SOR=0.847	GT:AD:DP:GQ:PL	1/1:0,332:332:99:10143,990,0
+NC_002945.4	3159182	.	G	A	7811.77	.	AC=2;AF=1.00;AN=2;DP=269;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.04;SOR=0.827	GT:AD:DP:GQ:PL	1/1:0,269:269:99:7840,802,0
+NC_002945.4	3173568	.	T	C	6936.77	.	AC=2;AF=1.00;AN=2;DP=202;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.86;SOR=1.052	GT:AD:DP:GQ:PL	1/1:0,199:199:99:6965,597,0
+NC_002945.4	3203316	.	T	C	10420.77	.	AC=2;AF=1.00;AN=2;DP=357;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.27;SOR=0.762	GT:AD:DP:GQ:PL	1/1:0,356:356:99:10449,1060,0
+NC_002945.4	3209298	.	N	.	.	.	.	GT	./.
+NC_002945.4	3209299	.	N	.	.	.	.	GT	./.
+NC_002945.4	3209300	.	N	.	.	.	.	GT	./.
+NC_002945.4	3209301	.	N	.	.	.	.	GT	./.
+NC_002945.4	3211854	.	T	C	6907.77	.	AC=2;AF=1.00;AN=2;DP=236;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.27;SOR=0.856	GT:AD:DP:GQ:PL	1/1:0,236:236:99:6936,702,0
+NC_002945.4	3219356	.	N	.	.	.	.	GT	./.
+NC_002945.4	3219357	.	N	.	.	.	.	GT	./.
+NC_002945.4	3225166	.	T	G	94.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.377;ClippingRankSum=0.000;DP=180;ExcessHet=3.0103;FS=228.442;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=0.53;ReadPosRankSum=3.077;SOR=7.903	GT:AD:DP:GQ:PL	0/1:129,51:180:99:123,0,2817
+NC_002945.4	3230333	.	G	A	5302.77	.	AC=2;AF=1.00;AN=2;DP=191;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.76;SOR=0.814	GT:AD:DP:GQ:PL	1/1:0,191:191:99:5331,567,0
+NC_002945.4	3247623	.	C	T	6755.77	.	AC=2;AF=1.00;AN=2;DP=234;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.25;SOR=1.234	GT:AD:DP:GQ:PL	1/1:0,231:231:99:6784,687,0
+NC_002945.4	3261792	.	A	G	12178.77	.	AC=2;AF=1.00;AN=2;DP=434;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.13;SOR=0.794	GT:AD:DP:GQ:PL	1/1:0,433:433:99:12207,1290,0
+NC_002945.4	3267690	.	A	G	8125.77	.	AC=2;AF=1.00;AN=2;DP=253;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.12;SOR=0.750	GT:AD:DP:GQ:PL	1/1:0,253:253:99:8154,753,0
+NC_002945.4	3270181	.	A	G	9105.77	.	AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.56;SOR=0.719	GT:AD:DP:GQ:PL	1/1:0,308:308:99:9134,919,0
+NC_002945.4	3282696	.	G	A	9245.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.564;ClippingRankSum=0.000;DP=339;ExcessHet=3.0103;FS=3.103;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.77;ReadPosRankSum=-0.405;SOR=0.301	GT:AD:DP:GQ:PL	1/1:1,332:333:99:9274,974,0
+NC_002945.4	3297745	.	A	T	938.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.263;ClippingRankSum=0.000;DP=114;ExcessHet=3.0103;FS=22.822;MLEAC=1;MLEAF=0.500;MQ=56.99;MQRankSum=-3.428;QD=8.23;ReadPosRankSum=-4.337;SOR=0.047	GT:AD:DP:GQ:PL	0/1:71,43:114:99:967,0,2866
+NC_002945.4	3329772	.	C	G	7731.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.925;ClippingRankSum=0.000;DP=257;ExcessHet=3.0103;FS=3.096;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=30.32;ReadPosRankSum=-0.608;SOR=0.299	GT:AD:DP:GQ:PL	1/1:1,254:255:99:7760,750,0
+NC_002945.4	3338298	.	C	G	3356.77	.	AC=2;AF=1.00;AN=2;DP=126;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.78;QD=27.07;SOR=1.197	GT:AD:DP:GQ:PL	1/1:0,124:124:99:3385,368,0
+NC_002945.4	3371156	.	A	G	9051.77	.	AC=2;AF=1.00;AN=2;DP=291;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.11;SOR=0.847	GT:AD:DP:GQ:PL	1/1:0,291:291:99:9080,866,0
+NC_002945.4	3394764	.	A	G	9595.77	.	AC=2;AF=1.00;AN=2;DP=330;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.26;SOR=0.769	GT:AD:DP:GQ:PL	1/1:0,328:328:99:9624,976,0
+NC_002945.4	3396621	.	G	C	8668.77	.	AC=2;AF=1.00;AN=2;DP=286;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=0.907	GT:AD:DP:GQ:PL	1/1:0,286:286:99:8697,854,0
+NC_002945.4	3399294	.	G	T	8108.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.840;ClippingRankSum=0.000;DP=272;ExcessHet=3.0103;FS=3.059;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.92;ReadPosRankSum=2.415;SOR=0.270	GT:AD:DP:GQ:PL	1/1:1,270:271:99:8137,795,0
+NC_002945.4	3421983	.	C	T	5464.77	.	AC=2;AF=1.00;AN=2;DP=170;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.12;SOR=2.069	GT:AD:DP:GQ:PL	1/1:0,165:165:99:5493,493,0
+NC_002945.4	3428078	.	C	T	5462.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.079;ClippingRankSum=0.000;DP=218;ExcessHet=3.0103;FS=26.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.41;ReadPosRankSum=3.211;SOR=1.197	GT:AD:DP:GQ:PL	1/1:6,209:215:99:5491,562,0
+NC_002945.4	3429376	.	A	C	5595.77	.	AC=2;AF=1.00;AN=2;DP=165;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.33;SOR=1.698	GT:AD:DP:GQ:PL	1/1:0,163:163:99:5624,488,0
+NC_002945.4	3439578	.	G	A	10250.77	.	AC=2;AF=1.00;AN=2;DP=359;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.88;SOR=0.909	GT:AD:DP:GQ:PL	1/1:0,355:355:99:10279,1056,0
+NC_002945.4	3450988	.	C	T	9125.77	.	AC=2;AF=1.00;AN=2;DP=307;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.92;SOR=1.156	GT:AD:DP:GQ:PL	1/1:0,305:305:99:9154,907,0
+NC_002945.4	3451869	.	C	A	8997.77	.	AC=2;AF=1.00;AN=2;DP=317;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.66;SOR=0.706	GT:AD:DP:GQ:PL	1/1:0,314:314:99:9026,929,0
+NC_002945.4	3464524	.	T	C	5370.77	.	AC=2;AF=1.00;AN=2;DP=139;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.51;SOR=5.361	GT:AD:DP:GQ:PL	1/1:0,138:138:99:5399,414,0
+NC_002945.4	3471404	.	A	G	11021.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.621;ClippingRankSum=0.000;DP=358;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=31.13;ReadPosRankSum=-0.717;SOR=1.272	GT:AD:DP:GQ:PL	1/1:2,352:354:99:11050,1033,0
+NC_002945.4	3482644	.	A	T	6350.77	.	AC=2;AF=1.00;AN=2;DP=220;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.27;SOR=0.861	GT:AD:DP:GQ:PL	1/1:0,217:217:99:6379,644,0
+NC_002945.4	3484836	.	A	G	9592.77	.	AC=2;AF=1.00;AN=2;DP=328;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.94;QD=29.43;SOR=0.782	GT:AD:DP:GQ:PL	1/1:0,326:326:99:9621,971,0
+NC_002945.4	3495510	.	C	T	7253.77	.	AC=2;AF=1.00;AN=2;DP=255;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.13;SOR=1.055	GT:AD:DP:GQ:PL	1/1:0,249:249:99:7282,738,0
+NC_002945.4	3521264	.	C	T	8800.77	.	AC=2;AF=1.00;AN=2;DP=309;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.57;SOR=0.774	GT:AD:DP:GQ:PL	1/1:0,308:308:99:8829,919,0
+NC_002945.4	3558883	.	G	C	7931.77	.	AC=2;AF=1.00;AN=2;DP=240;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.61;SOR=2.282	GT:AD:DP:GQ:PL	1/1:0,236:236:99:7960,702,0
+NC_002945.4	3574014	.	T	C	9000.77	.	AC=2;AF=1.00;AN=2;DP=290;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.14;SOR=1.227	GT:AD:DP:GQ:PL	1/1:0,289:289:99:9029,862,0
+NC_002945.4	3577163	.	G	T	9642.77	.	AC=2;AF=1.00;AN=2;DP=300;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.25;SOR=1.130	GT:AD:DP:GQ:PL	1/1:0,299:299:99:9671,893,0
+NC_002945.4	3626128	.	T	C	7529.77	.	AC=2;AF=1.00;AN=2;DP=239;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.51;SOR=0.826	GT:AD:DP:GQ:PL	1/1:0,239:239:99:7558,715,0
+NC_002945.4	3629370	.	G	A	8131.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.877;ClippingRankSum=0.000;DP=278;ExcessHet=3.0103;FS=3.268;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.25;ReadPosRankSum=2.075;SOR=0.423	GT:AD:DP:GQ:PL	1/1:1,277:278:99:8160,818,0
+NC_002945.4	3667823	.	A	G	10431.77	.	AC=2;AF=1.00;AN=2;DP=336;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.03;QD=31.05;SOR=0.742	GT:AD:DP:GQ:PL	1/1:0,336:336:99:10460,1004,0
+NC_002945.4	3695728	.	N	.	.	.	.	GT	./.
+NC_002945.4	3695729	.	N	.	.	.	.	GT	./.
+NC_002945.4	3695730	.	N	.	.	.	.	GT	./.
+NC_002945.4	3695731	.	N	.	.	.	.	GT	./.
+NC_002945.4	3695732	.	N	.	.	.	.	GT	./.
+NC_002945.4	3695733	.	N	.	.	.	.	GT	./.
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+NC_002945.4	3695735	.	N	.	.	.	.	GT	./.
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