# HG changeset patch
# User iuc
# Date 1487590542 18000
# Node ID bf8841b0a6b0a354f0e3c32bbdfaa9707124b357

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7

diff -r 000000000000 -r bf8841b0a6b0 extract_variants.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_variants.xml	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,79 @@
+<tool id="gvcftools_extract_variants" name="Extract Variants from gVCF files" version="0.1">
+  <description>Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.</description>
+
+  <requirements>
+      <requirement type="package" version="0.17.0">gvcftools</requirement>
+  </requirements>
+
+  <command detect_errors="aggressive">
+  <![CDATA[
+      extract_variants
+        #if str( $advanced.advanced_options_selector ) == 'true':
+         '${advanced.skip_header}' '${advanced.invert}'
+        #end if
+      < '${gvcf_input}' > '${vcf_output}'
+  ]]>]
+  </command>
+
+  <inputs>
+    <param name="gvcf_input" type="data" format="vcf" label="Variants (gVCF format)" />
+    <conditional name="advanced">
+      <param name="advanced_options_selector" type="select" label="Advanced options">
+        <option value="true">Show advanced options</option>
+        <option value="false" selected="True">Don't show advanced options</option>
+      </param>
+      <when value="true">
+        <param type="boolean" name="skip_header" argument="--skip-header"
+          truevalue="--skip-header" falsevalue=""
+          label="Write the variants output file without a header" />
+        <param type="boolean" argument="--invert"
+          truevalue="--invert" falsevalue=""
+          label="Invert the filter so that only non-variant records are output" />
+      </when>
+      <when value="false"></when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="vcf_output" format="vcf" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <output name="vcf_output" ftype="vcf" value="variants_output1.vcf" />
+    </test>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <param name="advanced_options_selector" value="true" />
+      <param name="skip_header" value="True" />
+      <output name="vcf_output" ftype="vcf" value="variants_noheader_output1.vcf" />
+    </test>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <param name="advanced_options_selector" value="true" />
+      <param name="invert" value="True" />
+      <output name="vcf_output" ftype="vcf" value="nonvariants_output1.vcf" />
+    </test>
+
+  </tests>
+
+  <help>
+    <![CDATA[
+    Extract variants from a gVCF field, removing all non-variant blocks to yield a smaller variant only VCF file.
+
+    From the `gvcftools`_ toolkit.
+
+    .. _gvcftools: https://sites.google.com/site/gvcftools/
+    ]]>
+  </help>
+  <citations>
+        <citation type="bibtex">
+           @unpublished{gvcftools,
+              author = {Illumina, Inc.},
+              title  = {gvcftools},
+              url    = {https://sites.google.com/site/gvcftools/}
+            }
+        </citation>
+  </citations>
+</tool>
diff -r 000000000000 -r bf8841b0a6b0 test-data/input1.gvcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.gvcf	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 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=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 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=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false 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 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null 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">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive)
+##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive)
+##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive)
+##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive)
+##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive)
+##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive)
+##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive)
+##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive)
+##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive)
+##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive)
+##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive)
+##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive)
+##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive)
+##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive)
+##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive)
+##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive)
+##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
+##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##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=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=gi|448814763|ref|NC_000962.3|,length=4411532>
+##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	./R_2117_866#L5-_.R
+gi|448814763|ref|NC_000962.3|	1	.	T	<NON_REF>	.	.	END=1976	GT:DP:GQ:MIN_DP:PL	0:97:99:51:0,1710
+gi|448814763|ref|NC_000962.3|	1977	.	A	G,<NON_REF>	1986	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2016,0,2016:0,0,11,42
+gi|448814763|ref|NC_000962.3|	1978	.	T	<NON_REF>	.	.	END=4012	GT:DP:GQ:MIN_DP:PL	0:90:99:52:0,1779
+gi|448814763|ref|NC_000962.3|	4013	.	T	C,<NON_REF>	2081	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2111,0,2111:0,0,29,24
+gi|448814763|ref|NC_000962.3|	4014	.	C	<NON_REF>	.	.	END=7361	GT:DP:GQ:MIN_DP:PL	0:70:99:35:0,1159
+gi|448814763|ref|NC_000962.3|	7362	.	G	C,<NON_REF>	3369	.	BaseQRankSum=1.693;ClippingRankSum=1.693;DP=88;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=0.827;ReadPosRankSum=1.614	GT:AD:DP:GQ:PL:SB	1:1,87,0:88:99:3399,0,3408:0,1,40,47
+gi|448814763|ref|NC_000962.3|	7363	.	A	<NON_REF>	.	.	END=7584	GT:DP:GQ:MIN_DP:PL	0:60:99:50:0,1746
+gi|448814763|ref|NC_000962.3|	7585	.	G	C,<NON_REF>	2294	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2324,0,2324:0,0,36,24
+gi|448814763|ref|NC_000962.3|	7586	.	C	<NON_REF>	.	.	END=9303	GT:DP:GQ:MIN_DP:PL	0:76:99:46:0,1601
+gi|448814763|ref|NC_000962.3|	9304	.	G	A,<NON_REF>	2343	.	DP=69;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2373,0,2373:0,0,31,38
+gi|448814763|ref|NC_000962.3|	9305	.	C	<NON_REF>	.	.	END=11310	GT:DP:GQ:MIN_DP:PL	0:69:99:19:0,644
+gi|448814763|ref|NC_000962.3|	11311	.	A	C,<NON_REF>	3627	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3657,0,3657:0,0,31,65
+gi|448814763|ref|NC_000962.3|	11312	.	G	<NON_REF>	.	.	END=11369	GT:DP:GQ:MIN_DP:PL	0:83:99:78:0,1800
+gi|448814763|ref|NC_000962.3|	11370	.	C	T,<NON_REF>	2699	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2729,0,2729:0,0,21,56
+gi|448814763|ref|NC_000962.3|	11371	.	C	<NON_REF>	.	.	END=11878	GT:DP:GQ:MIN_DP:PL	0:71:99:40:0,1215
+gi|448814763|ref|NC_000962.3|	11879	.	A	G,<NON_REF>	2659	.	DP=70;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2689,0,2689:0,0,36,33
+gi|448814763|ref|NC_000962.3|	11880	.	G	<NON_REF>	.	.	END=14784	GT:DP:GQ:MIN_DP:PL	0:71:99:27:0,765
+gi|448814763|ref|NC_000962.3|	14785	.	T	C,<NON_REF>	3506	.	DP=90;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,90,0:90:99:3536,0,3536:0,0,38,52
+gi|448814763|ref|NC_000962.3|	14786	.	G	<NON_REF>	.	.	END=21794	GT:DP:GQ:MIN_DP:PL	0:70:99:15:0,405
+gi|448814763|ref|NC_000962.3|	21795	.	G	A,<NON_REF>	784	.	DP=24;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:814,0,814:0,0,8,16
+gi|448814763|ref|NC_000962.3|	21796	.	C	<NON_REF>	.	.	END=24697	GT:DP:GQ:MIN_DP:PL	0:60:99:5:0,135
+gi|448814763|ref|NC_000962.3|	24698	.	GCCGCGTTGCTCGGGGTAA	G,<NON_REF>	1536.97	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.01;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1576,0,1576:0,0,25,11
+gi|448814763|ref|NC_000962.3|	24717	.	C	<NON_REF>	.	.	END=24717	GT:DP:GQ:MIN_DP:PL	0:38:0:38:0,0
+gi|448814763|ref|NC_000962.3|	24718	.	C	<NON_REF>	.	.	END=26958	GT:DP:GQ:MIN_DP:PL	0:60:99:26:0,852
+gi|448814763|ref|NC_000962.3|	26959	.	C	G,<NON_REF>	2474	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2504,0,2504:0,0,41,25
+gi|448814763|ref|NC_000962.3|	26960	.	C	<NON_REF>	.	.	END=29474	GT:DP:GQ:MIN_DP:PL	0:54:99:21:0,405
+gi|448814763|ref|NC_000962.3|	29475	.	T	<NON_REF>	.	.	END=29476	GT:DP:GQ:MIN_DP:PL	0:70:44:69:0,45
+gi|448814763|ref|NC_000962.3|	29477	.	A	<NON_REF>	.	.	END=29480	GT:DP:GQ:MIN_DP:PL	0:72:0:71:0,0
+gi|448814763|ref|NC_000962.3|	29481	.	T	<NON_REF>	.	.	END=29481	GT:DP:GQ:MIN_DP:PL	0:72:44:72:0,45
+gi|448814763|ref|NC_000962.3|	29482	.	CA	C,<NON_REF>	2528.97	.	DP=74;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.14;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2568,0,2568:0,0,34,38
+gi|448814763|ref|NC_000962.3|	29484	.	A	<NON_REF>	.	.	END=29484	GT:DP:GQ:MIN_DP:PL	0:74:0:74:0,0
+gi|448814763|ref|NC_000962.3|	29485	.	A	<NON_REF>	.	.	END=30518	GT:DP:GQ:MIN_DP:PL	0:78:99:26:0,798
+gi|448814763|ref|NC_000962.3|	30519	.	C	T,<NON_REF>	2289	.	BaseQRankSum=1.681;ClippingRankSum=0.026;DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.525;ReadPosRankSum=1.060	GT:AD:DP:GQ:PL:SB	1:1,66,0:67:99:2319,0,2329:1,0,47,19
+gi|448814763|ref|NC_000962.3|	30520	.	G	<NON_REF>	.	.	END=30687	GT:DP:GQ:MIN_DP:PL	0:66:99:54:0,1653
+gi|448814763|ref|NC_000962.3|	30688	.	T	G,<NON_REF>	2109	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2139,0,2139:0,0,30,26
+gi|448814763|ref|NC_000962.3|	30689	.	C	<NON_REF>	.	.	END=30942	GT:DP:GQ:MIN_DP:PL	0:49:99:29:0,959
+gi|448814763|ref|NC_000962.3|	30943	.	C	T,<NON_REF>	1534	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1564,0,1564:0,0,28,21
+gi|448814763|ref|NC_000962.3|	30944	.	C	<NON_REF>	.	.	END=31076	GT:DP:GQ:MIN_DP:PL	0:58:99:43:0,1528
+gi|448814763|ref|NC_000962.3|	31077	.	C	T,<NON_REF>	1499	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,43,0:43:99:1529,0,1529:0,0,24,19
+gi|448814763|ref|NC_000962.3|	31078	.	A	<NON_REF>	.	.	END=32341	GT:DP:GQ:MIN_DP:PL	0:69:99:39:0,135
+gi|448814763|ref|NC_000962.3|	32342	.	G	<NON_REF>	.	.	END=32348	GT:DP:GQ:MIN_DP:PL	0:41:0:41:0,0
+gi|448814763|ref|NC_000962.3|	32349	.	CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG	C,<NON_REF>	3070.97	.	DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=65.20;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,70,0:70:99:3110,0,3110:0,0,35,35
+gi|448814763|ref|NC_000962.3|	32387	.	C	<NON_REF>	.	.	END=34043	GT:DP:GQ:MIN_DP:PL	0:60:99:26:0,900
+gi|448814763|ref|NC_000962.3|	34044	.	T	C,<NON_REF>	3703	.	DP=94;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,94,0:94:99:3733,0,3733:0,0,60,34
+gi|448814763|ref|NC_000962.3|	34045	.	G	<NON_REF>	.	.	END=37030	GT:DP:GQ:MIN_DP:PL	0:89:99:30:0,900
+gi|448814763|ref|NC_000962.3|	37031	.	C	G,<NON_REF>	1773	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1803,0,1803:0,0,22,24
+gi|448814763|ref|NC_000962.3|	37032	.	T	<NON_REF>	.	.	END=37909	GT:DP:GQ:MIN_DP:PL	0:58:99:36:0,1260
+gi|448814763|ref|NC_000962.3|	37910	.	C	A,<NON_REF>	3793	.	DP=113;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3823,0,3823:0,0,62,51
+gi|448814763|ref|NC_000962.3|	37911	.	C	<NON_REF>	.	.	END=39218	GT:DP:GQ:MIN_DP:PL	0:65:99:30:0,180
+gi|448814763|ref|NC_000962.3|	39219	.	G	<NON_REF>	.	.	END=39221	GT:DP:GQ:MIN_DP:PL	0:49:0:48:0,0
+gi|448814763|ref|NC_000962.3|	39222	.	G	<NON_REF>	.	.	END=39222	GT:DP:GQ:MIN_DP:PL	0:52:99:52:0,135
+gi|448814763|ref|NC_000962.3|	39223	.	GC	G,<NON_REF>	1460.97	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1500,0,1500:0,0,19,27
+gi|448814763|ref|NC_000962.3|	39225	.	C	<NON_REF>	.	.	END=39225	GT:DP:GQ:MIN_DP:PL	0:49:0:49:0,0
+gi|448814763|ref|NC_000962.3|	39226	.	C	<NON_REF>	.	.	END=42966	GT:DP:GQ:MIN_DP:PL	0:46:99:20:0,633
+gi|448814763|ref|NC_000962.3|	42967	.	G	C,<NON_REF>	2609	.	DP=67;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,67,0:67:99:2639,0,2639:0,0,15,52
+gi|448814763|ref|NC_000962.3|	42968	.	G	<NON_REF>	.	.	END=50556	GT:DP:GQ:MIN_DP:PL	0:65:99:15:0,315
+gi|448814763|ref|NC_000962.3|	50557	.	T	C,<NON_REF>	2896	.	DP=73;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,73,0:73:99:2926,0,2926:0,0,43,30
+gi|448814763|ref|NC_000962.3|	50558	.	G	<NON_REF>	.	.	END=51948	GT:DP:GQ:MIN_DP:PL	0:73:99:39:0,1288
+gi|448814763|ref|NC_000962.3|	51949	.	A	G,<NON_REF>	3374	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,76,0:76:99:3404,0,3404:0,0,33,43
+gi|448814763|ref|NC_000962.3|	51950	.	C	<NON_REF>	.	.	END=51953	GT:DP:GQ:MIN_DP:PL	0:77:99:75:0,1800
+gi|448814763|ref|NC_000962.3|	51954	.	T	A,<NON_REF>	3329	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,71,0:71:99:3359,0,3359:0,0,29,42
+gi|448814763|ref|NC_000962.3|	51955	.	T	<NON_REF>	.	.	END=53784	GT:DP:GQ:MIN_DP:PL	0:57:99:11:0,364
+gi|448814763|ref|NC_000962.3|	53785	.	C	G,<NON_REF>	3639	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3669,0,3669:0,0,54,42
+gi|448814763|ref|NC_000962.3|	53786	.	G	<NON_REF>	.	.	END=54393	GT:DP:GQ:MIN_DP:PL	0:95:99:64:0,1800
+gi|448814763|ref|NC_000962.3|	54394	.	A	G,<NON_REF>	3218	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3248,0,3248:0,0,40,43
+gi|448814763|ref|NC_000962.3|	54395	.	G	<NON_REF>	.	.	END=55533	GT:DP:GQ:MIN_DP:PL	0:72:99:19:0,270
+gi|448814763|ref|NC_000962.3|	55534	.	G	<NON_REF>	.	.	END=55552	GT:DP:GQ:MIN_DP:PL	0:25:0:20:0,0
+gi|448814763|ref|NC_000962.3|	55553	.	C	CCGCCGT,<NON_REF>	942.97	.	DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=74.16;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:982,0,982:0,0,8,16
+gi|448814763|ref|NC_000962.3|	55554	.	C	<NON_REF>	.	.	END=55554	GT:DP:GQ:MIN_DP:PL	0:26:0:26:0,0
+gi|448814763|ref|NC_000962.3|	55555	.	G	<NON_REF>	.	.	END=57392	GT:DP:GQ:MIN_DP:PL	0:48:99:14:0,422
+gi|448814763|ref|NC_000962.3|	57393	.	A	T,<NON_REF>	1304	.	DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1334,0,1334:0,0,32,4
+gi|448814763|ref|NC_000962.3|	57394	.	C	<NON_REF>	.	.	END=62048	GT:DP:GQ:MIN_DP:PL	0:68:99:22:0,720
+gi|448814763|ref|NC_000962.3|	62049	.	A	G,<NON_REF>	1820	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1850,0,1850:0,0,24,24
+gi|448814763|ref|NC_000962.3|	62050	.	G	<NON_REF>	.	.	END=62656	GT:DP:GQ:MIN_DP:PL	0:86:99:37:0,1231
+gi|448814763|ref|NC_000962.3|	62657	.	G	A,<NON_REF>	3950	.	DP=109;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,109,0:109:99:3980,0,3980:0,0,64,45
+gi|448814763|ref|NC_000962.3|	62658	.	A	<NON_REF>	.	.	END=66284	GT:DP:GQ:MIN_DP:PL	0:87:99:26:0,900
+gi|448814763|ref|NC_000962.3|	66285	.	C	G,<NON_REF>	2074	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2104,0,2104:0,0,20,33
+gi|448814763|ref|NC_000962.3|	66286	.	G	<NON_REF>	.	.	END=69870	GT:DP:GQ:MIN_DP:PL	0:57:99:17:0,495
+gi|448814763|ref|NC_000962.3|	69871	.	C	T,<NON_REF>	3532	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3562,0,3562:0,0,42,59
+gi|448814763|ref|NC_000962.3|	69872	.	T	<NON_REF>	.	.	END=69988	GT:DP:GQ:MIN_DP:PL	0:69:99:53:0,1800
+gi|448814763|ref|NC_000962.3|	69989	.	G	A,<NON_REF>	1569	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,50,0:50:99:1599,0,1599:0,0,16,34
+gi|448814763|ref|NC_000962.3|	69990	.	T	<NON_REF>	.	.	END=70815	GT:DP:GQ:MIN_DP:PL	0:76:99:36:0,1125
+gi|448814763|ref|NC_000962.3|	70816	.	A	G,<NON_REF>	3136	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3166,0,3166:0,0,59,24
+gi|448814763|ref|NC_000962.3|	70817	.	A	<NON_REF>	.	.	END=71335	GT:DP:GQ:MIN_DP:PL	0:72:99:33:0,900
+gi|448814763|ref|NC_000962.3|	71336	.	G	C,<NON_REF>	1177	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1207,0,1207:0,0,25,5
+gi|448814763|ref|NC_000962.3|	71337	.	C	<NON_REF>	.	.	END=71583	GT:DP:GQ:MIN_DP:PL	0:40:99:8:0,180
+gi|448814763|ref|NC_000962.3|	71584	.	C	CCGAGCGCTGTTCTGGCGCTAATCTGACGCTAGAATAG,<NON_REF>	3237.97	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.86;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:3277,0,3287:0,0,28,19
+gi|448814763|ref|NC_000962.3|	71585	.	C	<NON_REF>	.	.	END=75263	GT:DP:GQ:MIN_DP:PL	0:78:99:28:0,389
+gi|448814763|ref|NC_000962.3|	75264	.	C	T,<NON_REF>	2055	.	DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,58,0:58:99:2085,0,2085:0,0,24,34
+gi|448814763|ref|NC_000962.3|	75265	.	T	<NON_REF>	.	.	END=75939	GT:DP:GQ:MIN_DP:PL	0:56:99:34:0,1161
+gi|448814763|ref|NC_000962.3|	75940	.	G	C,<NON_REF>	2042	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2072,0,2072:0,0,32,23
+gi|448814763|ref|NC_000962.3|	75941	.	T	<NON_REF>	.	.	END=80615	GT:DP:GQ:MIN_DP:PL	0:65:99:24:0,135
+gi|448814763|ref|NC_000962.3|	80616	.	C	G,<NON_REF>	3150	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:3180,0,3180:0,0,39,42
+gi|448814763|ref|NC_000962.3|	80617	.	T	<NON_REF>	.	.	END=83981	GT:DP:GQ:MIN_DP:PL	0:72:99:31:0,1146
+gi|448814763|ref|NC_000962.3|	83982	.	A	G,<NON_REF>	3138	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,82,0:82:99:3168,0,3168:0,0,38,44
+gi|448814763|ref|NC_000962.3|	83983	.	A	<NON_REF>	.	.	END=86575	GT:DP:GQ:MIN_DP:PL	0:67:99:27:0,900
+gi|448814763|ref|NC_000962.3|	86576	.	G	A,<NON_REF>	2322	.	DP=65;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,65,0:65:99:2352,0,2352:0,0,31,34
+gi|448814763|ref|NC_000962.3|	86577	.	A	<NON_REF>	.	.	END=92198	GT:DP:GQ:MIN_DP:PL	0:47:99:5:0,135
+gi|448814763|ref|NC_000962.3|	92199	.	T	G,<NON_REF>	697	.	DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,20,0:20:99:727,0,727:0,0,15,5
+gi|448814763|ref|NC_000962.3|	92200	.	C	<NON_REF>	.	.	END=95590	GT:DP:GQ:MIN_DP:PL	0:46:99:20:0,756
+gi|448814763|ref|NC_000962.3|	95591	.	G	T,<NON_REF>	2735	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2765,0,2765:0,0,29,48
+gi|448814763|ref|NC_000962.3|	95592	.	A	<NON_REF>	.	.	END=97387	GT:DP:GQ:MIN_DP:PL	0:62:99:25:0,675
+gi|448814763|ref|NC_000962.3|	97388	.	G	T,<NON_REF>	3943	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3973,0,3973:0,0,57,56
+gi|448814763|ref|NC_000962.3|	97389	.	A	<NON_REF>	.	.	END=103835	GT:DP:GQ:MIN_DP:PL	0:55:99:12:0,423
+gi|448814763|ref|NC_000962.3|	103836	.	G	T,<NON_REF>	413	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.44;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:443,0,443:0,0,0,12
+gi|448814763|ref|NC_000962.3|	103837	.	T	<NON_REF>	.	.	END=103883	GT:DP:GQ:MIN_DP:PL	0:10:99:8:0,135
+gi|448814763|ref|NC_000962.3|	103884	.	G	<NON_REF>	.	.	END=103888	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
+gi|448814763|ref|NC_000962.3|	103889	.	G	<NON_REF>	.	.	END=103894	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	103895	.	G	<NON_REF>	.	.	END=104531	GT:DP:GQ:MIN_DP:PL	0:0:0:0:0,0
+gi|448814763|ref|NC_000962.3|	104532	.	T	<NON_REF>	.	.	END=104532	GT:DP:GQ:MIN_DP:PL	0:1:34:1:0,35
+gi|448814763|ref|NC_000962.3|	104533	.	T	<NON_REF>	.	.	END=104533	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	104534	.	C	<NON_REF>	.	.	END=104534	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	104535	.	G	<NON_REF>	.	.	END=104535	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	104536	.	G	<NON_REF>	.	.	END=104536	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	104537	.	T	<NON_REF>	.	.	END=104537	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	104538	.	G	<NON_REF>	.	.	END=104538	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	104539	.	T	<NON_REF>	.	.	END=104539	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	104540	.	C	<NON_REF>	.	.	END=104540	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	104541	.	G	<NON_REF>	.	.	END=104541	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	104542	.	G	<NON_REF>	.	.	END=104542	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	104543	.	T	<NON_REF>	.	.	END=104543	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	104544	.	G	<NON_REF>	.	.	END=104544	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	104545	.	A	<NON_REF>	.	.	END=104545	GT:DP:GQ:MIN_DP:PL	0:1:33:1:0,34
+gi|448814763|ref|NC_000962.3|	104546	.	G	<NON_REF>	.	.	END=104546	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	104547	.	G	<NON_REF>	.	.	END=104547	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
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+gi|448814763|ref|NC_000962.3|	150186	.	C	<NON_REF>	.	.	END=150197	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	150198	.	T	<NON_REF>	.	.	END=150198	GT:DP:GQ:MIN_DP:PL	0:1:27:1:0,28
+gi|448814763|ref|NC_000962.3|	150199	.	G	<NON_REF>	.	.	END=150220	GT:DP:GQ:MIN_DP:PL	0:1:0:0:0,0
+gi|448814763|ref|NC_000962.3|	150221	.	A	<NON_REF>	.	.	END=150221	GT:DP:GQ:MIN_DP:PL	0:1:24:1:0,25
+gi|448814763|ref|NC_000962.3|	150222	.	T	<NON_REF>	.	.	END=150222	GT:DP:GQ:MIN_DP:PL	0:1:19:1:0,20
+gi|448814763|ref|NC_000962.3|	150223	.	G	<NON_REF>	.	.	END=150223	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
+gi|448814763|ref|NC_000962.3|	150224	.	C	<NON_REF>	.	.	END=150224	GT:DP:GQ:MIN_DP:PL	0:2:63:2:0,63
+gi|448814763|ref|NC_000962.3|	150225	.	C	<NON_REF>	.	.	END=150225	GT:DP:GQ:MIN_DP:PL	0:2:70:2:0,71
+gi|448814763|ref|NC_000962.3|	150226	.	A	<NON_REF>	.	.	END=150227	GT:DP:GQ:MIN_DP:PL	0:2:67:2:0,63
+gi|448814763|ref|NC_000962.3|	150228	.	C	<NON_REF>	.	.	END=150228	GT:DP:GQ:MIN_DP:PL	0:2:72:2:0,73
+gi|448814763|ref|NC_000962.3|	150229	.	A	<NON_REF>	.	.	END=150229	GT:DP:GQ:MIN_DP:PL	0:2:55:2:0,55
+gi|448814763|ref|NC_000962.3|	150230	.	T	<NON_REF>	.	.	END=150230	GT:DP:GQ:MIN_DP:PL	0:2:56:2:0,56
+gi|448814763|ref|NC_000962.3|	150231	.	C	<NON_REF>	.	.	END=150231	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	150232	.	G	<NON_REF>	.	.	END=150232	GT:DP:GQ:MIN_DP:PL	0:2:60:2:0,60
+gi|448814763|ref|NC_000962.3|	150233	.	T	<NON_REF>	.	.	END=150233	GT:DP:GQ:MIN_DP:PL	0:2:71:2:0,72
+gi|448814763|ref|NC_000962.3|	150234	.	C	<NON_REF>	.	.	END=150234	GT:DP:GQ:MIN_DP:PL	0:2:65:2:0,66
+gi|448814763|ref|NC_000962.3|	150235	.	A	<NON_REF>	.	.	END=150236	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,99
+gi|448814763|ref|NC_000962.3|	150237	.	C	<NON_REF>	.	.	END=150239	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	150240	.	T	<NON_REF>	.	.	END=150240	GT:DP:GQ:MIN_DP:PL	0:3:39:3:0,40
+gi|448814763|ref|NC_000962.3|	150241	.	G	<NON_REF>	.	.	END=150242	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,135
+gi|448814763|ref|NC_000962.3|	150243	.	A	<NON_REF>	.	.	END=150243	GT:DP:GQ:MIN_DP:PL	0:3:98:3:0,98
+gi|448814763|ref|NC_000962.3|	150244	.	G	<NON_REF>	.	.	END=150258	GT:DP:GQ:MIN_DP:PL	0:5:99:4:0,134
+gi|448814763|ref|NC_000962.3|	150259	.	G	<NON_REF>	.	.	END=150260	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
+gi|448814763|ref|NC_000962.3|	150261	.	T	<NON_REF>	.	.	END=150261	GT:DP:GQ:MIN_DP:PL	0:4:65:4:0,66
+gi|448814763|ref|NC_000962.3|	150262	.	G	<NON_REF>	.	.	END=150269	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	150270	.	C	<NON_REF>	.	.	END=150270	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,79
+gi|448814763|ref|NC_000962.3|	150271	.	G	<NON_REF>	.	.	END=150272	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,81
+gi|448814763|ref|NC_000962.3|	150273	.	T	<NON_REF>	.	.	END=150275	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	150276	.	C	<NON_REF>	.	.	END=150276	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	150277	.	G	<NON_REF>	.	.	END=150286	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	150287	.	A	<NON_REF>	.	.	END=150287	GT:DP:GQ:MIN_DP:PL	0:1:22:1:0,23
+gi|448814763|ref|NC_000962.3|	150288	.	C	<NON_REF>	.	.	END=150288	GT:DP:GQ:MIN_DP:PL	0:1:33:1:0,34
+gi|448814763|ref|NC_000962.3|	150289	.	G	<NON_REF>	.	.	END=150289	GT:DP:GQ:MIN_DP:PL	0:1:32:1:0,33
+gi|448814763|ref|NC_000962.3|	150290	.	G	<NON_REF>	.	.	END=150290	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	150291	.	C	<NON_REF>	.	.	END=150291	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,80
+gi|448814763|ref|NC_000962.3|	150292	.	G	<NON_REF>	.	.	END=150292	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,117
+gi|448814763|ref|NC_000962.3|	150293	.	A	<NON_REF>	.	.	END=150293	GT:DP:GQ:MIN_DP:PL	0:3:88:3:0,88
+gi|448814763|ref|NC_000962.3|	150294	.	C	<NON_REF>	.	.	END=150317	GT:DP:GQ:MIN_DP:PL	0:5:99:3:0,106
+gi|448814763|ref|NC_000962.3|	150318	.	A	<NON_REF>	.	.	END=150319	GT:DP:GQ:MIN_DP:PL	0:6:44:6:0,45
+gi|448814763|ref|NC_000962.3|	150320	.	A	<NON_REF>	.	.	END=150325	GT:DP:GQ:MIN_DP:PL	0:6:0:5:0,0
+gi|448814763|ref|NC_000962.3|	150326	.	CAATCGGCCT	C,<NON_REF>	140.97	.	DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=59.60;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,4,0:4:99:180,0,180:0,0,2,2
+gi|448814763|ref|NC_000962.3|	150336	.	C	<NON_REF>	.	.	END=150336	GT:DP:GQ:MIN_DP:PL	0:4:0:4:0,0
+gi|448814763|ref|NC_000962.3|	150337	.	G	<NON_REF>	.	.	END=150337	GT:DP:GQ:MIN_DP:PL	0:5:99:5:0,180
+gi|448814763|ref|NC_000962.3|	150338	.	G	<NON_REF>	.	.	END=150338	GT:DP:GQ:MIN_DP:PL	0:5:44:5:0,45
+gi|448814763|ref|NC_000962.3|	150339	.	C	<NON_REF>	.	.	END=150345	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
+gi|448814763|ref|NC_000962.3|	150346	.	G	<NON_REF>	.	.	END=150355	GT:DP:GQ:MIN_DP:PL	0:5:99:5:0,135
+gi|448814763|ref|NC_000962.3|	150356	.	A	<NON_REF>	.	.	END=150356	GT:DP:GQ:MIN_DP:PL	0:5:79:5:0,79
+gi|448814763|ref|NC_000962.3|	150357	.	C	<NON_REF>	.	.	END=150593	GT:DP:GQ:MIN_DP:PL	0:8:99:3:0,101
+gi|448814763|ref|NC_000962.3|	150594	.	C	<NON_REF>	.	.	END=150603	GT:DP:GQ:MIN_DP:PL	0:6:44:4:0,45
+gi|448814763|ref|NC_000962.3|	150604	.	G	<NON_REF>	.	.	END=150895	GT:DP:GQ:MIN_DP:PL	0:12:99:4:0,109
+gi|448814763|ref|NC_000962.3|	150896	.	C	<NON_REF>	.	.	END=150896	GT:DP:GQ:MIN_DP:PL	0:20:0:20:0,0
+gi|448814763|ref|NC_000962.3|	150897	.	C	<NON_REF>	.	.	END=150903	GT:DP:GQ:MIN_DP:PL	0:22:99:20:0,144
+gi|448814763|ref|NC_000962.3|	150904	.	A	<NON_REF>	.	.	END=150904	GT:DP:GQ:MIN_DP:PL	0:19:51:19:0,51
+gi|448814763|ref|NC_000962.3|	150905	.	C	<NON_REF>	.	.	END=151176	GT:DP:GQ:MIN_DP:PL	0:41:99:10:0,149
+gi|448814763|ref|NC_000962.3|	151177	.	G	C,<NON_REF>	2127	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2157,0,2157:0,0,37,19
+gi|448814763|ref|NC_000962.3|	151178	.	T	<NON_REF>	.	.	END=154282	GT:DP:GQ:MIN_DP:PL	0:61:99:27:0,951
+gi|448814763|ref|NC_000962.3|	154283	.	T	C,<NON_REF>	2901	.	BaseQRankSum=1.646;ClippingRankSum=-0.909;DP=80;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.73;MQ0=0;MQRankSum=-1.213;ReadPosRankSum=1.342	GT:AD:DP:GQ:PL:SB	1:1,79,0:80:99:2931,0,2955:1,0,38,41
+gi|448814763|ref|NC_000962.3|	154284	.	C	<NON_REF>	.	.	END=155292	GT:DP:GQ:MIN_DP:PL	0:62:99:31:0,1080
+gi|448814763|ref|NC_000962.3|	155293	.	G	A,<NON_REF>	1652	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1682,0,1682:0,0,27,22
+gi|448814763|ref|NC_000962.3|	155294	.	G	<NON_REF>	.	.	END=163572	GT:DP:GQ:MIN_DP:PL	0:57:99:16:0,405
+gi|448814763|ref|NC_000962.3|	163573	.	A	C,<NON_REF>	1809	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1839,0,1839:0,0,23,25
+gi|448814763|ref|NC_000962.3|	163574	.	G	<NON_REF>	.	.	END=174683	GT:DP:GQ:MIN_DP:PL	0:55:99:13:0,450
+gi|448814763|ref|NC_000962.3|	174684	.	C	A,<NON_REF>	1780	.	DP=52;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,52,0:52:99:1810,0,1810:0,0,30,22
+gi|448814763|ref|NC_000962.3|	174685	.	G	<NON_REF>	.	.	END=177595	GT:DP:GQ:MIN_DP:PL	0:62:99:27:0,810
+gi|448814763|ref|NC_000962.3|	177596	.	T	C,<NON_REF>	2967	.	DP=78;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,78,0:78:99:2997,0,2997:0,0,63,15
+gi|448814763|ref|NC_000962.3|	177597	.	C	<NON_REF>	.	.	END=177856	GT:DP:GQ:MIN_DP:PL	0:72:99:39:0,1170
+gi|448814763|ref|NC_000962.3|	177857	.	G	A,<NON_REF>	1506	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,42,0:42:99:1536,0,1536:0,0,1,41
+gi|448814763|ref|NC_000962.3|	177858	.	C	<NON_REF>	.	.	END=178945	GT:DP:GQ:MIN_DP:PL	0:82:99:40:0,1417
+gi|448814763|ref|NC_000962.3|	178946	.	C	T,<NON_REF>	1368	.	DP=40;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,40,0:40:99:1398,0,1398:0,0,12,28
+gi|448814763|ref|NC_000962.3|	178947	.	G	<NON_REF>	.	.	END=187583	GT:DP:GQ:MIN_DP:PL	0:63:99:7:0,225
+gi|448814763|ref|NC_000962.3|	187584	.	A	G,<NON_REF>	2307	.	DP=60;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2337,0,2337:0,0,29,31
+gi|448814763|ref|NC_000962.3|	187585	.	A	<NON_REF>	.	.	END=187737	GT:DP:GQ:MIN_DP:PL	0:59:99:31:0,905
+gi|448814763|ref|NC_000962.3|	187738	.	G	A,<NON_REF>	2535	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2565,0,2565:0,0,36,36
+gi|448814763|ref|NC_000962.3|	187739	.	T	<NON_REF>	.	.	END=188799	GT:DP:GQ:MIN_DP:PL	0:83:99:14:0,180
+gi|448814763|ref|NC_000962.3|	188800	.	T	C,<NON_REF>	1495	.	DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,41,0:41:99:1525,0,1525:0,0,20,21
+gi|448814763|ref|NC_000962.3|	188801	.	C	<NON_REF>	.	.	END=191852	GT:DP:GQ:MIN_DP:PL	0:56:99:20:0,419
+gi|448814763|ref|NC_000962.3|	191853	.	A	G,<NON_REF>	2101	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2131,0,2131:0,0,21,34
+gi|448814763|ref|NC_000962.3|	191854	.	C	<NON_REF>	.	.	END=194680	GT:DP:GQ:MIN_DP:PL	0:63:99:10:0,347
+gi|448814763|ref|NC_000962.3|	194681	.	G	C,<NON_REF>	1539	.	DP=39;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,39,0:39:99:1569,0,1569:0,0,13,26
+gi|448814763|ref|NC_000962.3|	194682	.	A	<NON_REF>	.	.	END=196641	GT:DP:GQ:MIN_DP:PL	0:75:99:28:0,810
+gi|448814763|ref|NC_000962.3|	196642	.	C	T,<NON_REF>	4724	.	DP=132;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,132,0:132:99:4754,0,4754:0,0,59,73
+gi|448814763|ref|NC_000962.3|	196643	.	C	<NON_REF>	.	.	END=206338	GT:DP:GQ:MIN_DP:PL	0:75:99:12:0,270
+gi|448814763|ref|NC_000962.3|	206339	.	T	C,<NON_REF>	2188	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2218,0,2218:0,0,33,24
+gi|448814763|ref|NC_000962.3|	206340	.	G	<NON_REF>	.	.	END=220049	GT:DP:GQ:MIN_DP:PL	0:62:99:9:0,225
+gi|448814763|ref|NC_000962.3|	220050	.	C	T,<NON_REF>	981	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1011,0,1011:0,0,3,25
+gi|448814763|ref|NC_000962.3|	220051	.	A	<NON_REF>	.	.	END=223941	GT:DP:GQ:MIN_DP:PL	0:61:99:9:0,315
+gi|448814763|ref|NC_000962.3|	223942	.	T	C,<NON_REF>	486	.	DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,13,0:13:99:516,0,516:0,0,10,3
+gi|448814763|ref|NC_000962.3|	223943	.	C	<NON_REF>	.	.	END=225322	GT:DP:GQ:MIN_DP:PL	0:69:99:13:0,456
+gi|448814763|ref|NC_000962.3|	225323	.	T	C,<NON_REF>	2159	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2189,0,2189:0,0,29,28
+gi|448814763|ref|NC_000962.3|	225324	.	G	<NON_REF>	.	.	END=227097	GT:DP:GQ:MIN_DP:PL	0:88:99:43:0,1575
+gi|448814763|ref|NC_000962.3|	227098	.	T	C,<NON_REF>	2543	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2573,0,2573:0,0,31,35
+gi|448814763|ref|NC_000962.3|	227099	.	G	<NON_REF>	.	.	END=231113	GT:DP:GQ:MIN_DP:PL	0:59:99:17:0,540
+gi|448814763|ref|NC_000962.3|	231114	.	C	G,<NON_REF>	4042	.	DP=106;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,106,0:106:99:4072,0,4072:0,0,54,52
+gi|448814763|ref|NC_000962.3|	231115	.	C	<NON_REF>	.	.	END=232573	GT:DP:GQ:MIN_DP:PL	0:56:99:23:0,730
+gi|448814763|ref|NC_000962.3|	232574	.	G	T,<NON_REF>	2181	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,61,0:61:99:2211,0,2211:0,0,32,29
+gi|448814763|ref|NC_000962.3|	232575	.	C	<NON_REF>	.	.	END=234476	GT:DP:GQ:MIN_DP:PL	0:59:99:13:0,135
+gi|448814763|ref|NC_000962.3|	234477	.	T	G,<NON_REF>	329	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:359,0,359:0,0,8,4
+gi|448814763|ref|NC_000962.3|	234478	.	C	<NON_REF>	.	.	END=234482	GT:DP:GQ:MIN_DP:PL	0:12:99:11:0,135
+gi|448814763|ref|NC_000962.3|	234483	.	A	<NON_REF>	.	.	END=234485	GT:DP:GQ:MIN_DP:PL	0:8:89:8:0,90
+gi|448814763|ref|NC_000962.3|	234486	.	G	<NON_REF>	.	.	END=234487	GT:DP:GQ:MIN_DP:PL	0:16:44:12:0,45
+gi|448814763|ref|NC_000962.3|	234488	.	C	<NON_REF>	.	.	END=234490	GT:DP:GQ:MIN_DP:PL	0:16:0:16:0,0
+gi|448814763|ref|NC_000962.3|	234491	.	T	<NON_REF>	.	.	END=234491	GT:DP:GQ:MIN_DP:PL	0:17:44:17:0,45
+gi|448814763|ref|NC_000962.3|	234492	.	T	<NON_REF>	.	.	END=234492	GT:DP:GQ:MIN_DP:PL	0:18:89:18:0,90
+gi|448814763|ref|NC_000962.3|	234493	.	C	<NON_REF>	.	.	END=234495	GT:DP:GQ:MIN_DP:PL	0:21:99:20:0,225
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+gi|448814763|ref|NC_000962.3|	261869	.	T	C,<NON_REF>	394	.	DP=11;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,11,0:11:99:424,0,424:0,0,2,9
+gi|448814763|ref|NC_000962.3|	261870	.	G	<NON_REF>	.	.	END=265474	GT:DP:GQ:MIN_DP:PL	0:63:99:6:0,212
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+gi|448814763|ref|NC_000962.3|	265476	.	A	<NON_REF>	.	.	END=265553	GT:DP:GQ:MIN_DP:PL	0:113:99:105:0,1800
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+gi|448814763|ref|NC_000962.3|	265555	.	G	<NON_REF>	.	.	END=265967	GT:DP:GQ:MIN_DP:PL	0:72:99:37:0,1314
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+gi|448814763|ref|NC_000962.3|	265969	.	A	<NON_REF>	.	.	END=278680	GT:DP:GQ:MIN_DP:PL	0:59:99:14:0,427
+gi|448814763|ref|NC_000962.3|	278681	.	C	G,<NON_REF>	2284	.	DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,59,0:59:99:2314,0,2314:0,0,36,23
+gi|448814763|ref|NC_000962.3|	278682	.	A	<NON_REF>	.	.	END=279555	GT:DP:GQ:MIN_DP:PL	0:69:99:4:0,135
+gi|448814763|ref|NC_000962.3|	279556	.	C	<NON_REF>	.	.	END=279557	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
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+gi|448814763|ref|NC_000962.3|	279562	.	C	<NON_REF>	.	.	END=279563	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	279564	.	T	<NON_REF>	.	.	END=283613	GT:DP:GQ:MIN_DP:PL	0:54:99:5:0,135
+gi|448814763|ref|NC_000962.3|	283614	.	T	C,<NON_REF>	1794	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:1824,0,1824:0,0,30,17
+gi|448814763|ref|NC_000962.3|	283615	.	A	<NON_REF>	.	.	END=284622	GT:DP:GQ:MIN_DP:PL	0:37:99:17:0,540
+gi|448814763|ref|NC_000962.3|	284623	.	G	A,<NON_REF>	1019	.	DP=31;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,31,0:31:99:1049,0,1049:0,0,22,9
+gi|448814763|ref|NC_000962.3|	284624	.	G	<NON_REF>	.	.	END=285771	GT:DP:GQ:MIN_DP:PL	0:26:99:9:0,305
+gi|448814763|ref|NC_000962.3|	285772	.	A	C,<NON_REF>	1085	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1115,0,1115:0,0,11,17
+gi|448814763|ref|NC_000962.3|	285773	.	G	<NON_REF>	.	.	END=285870	GT:DP:GQ:MIN_DP:PL	0:24:99:19:0,585
+gi|448814763|ref|NC_000962.3|	285871	.	A	G,<NON_REF>	1112	.	DP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,29,0:29:99:1142,0,1142:0,0,19,10
+gi|448814763|ref|NC_000962.3|	285872	.	A	<NON_REF>	.	.	END=293623	GT:DP:GQ:MIN_DP:PL	0:51:99:9:0,135
+gi|448814763|ref|NC_000962.3|	293624	.	T	<NON_REF>	.	.	END=293627	GT:DP:GQ:MIN_DP:PL	0:47:0:46:0,0
+gi|448814763|ref|NC_000962.3|	293628	.	A	AC,<NON_REF>	1458.97	.	DP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1498,0,1498:0,0,36,10
+gi|448814763|ref|NC_000962.3|	293629	.	C	<NON_REF>	.	.	END=293629	GT:DP:GQ:MIN_DP:PL	0:51:0:51:0,0
+gi|448814763|ref|NC_000962.3|	293630	.	C	<NON_REF>	.	.	END=301289	GT:DP:GQ:MIN_DP:PL	0:78:99:19:0,391
+gi|448814763|ref|NC_000962.3|	301290	.	G	A,<NON_REF>	2691	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:2721,0,2721:0,0,41,40
+gi|448814763|ref|NC_000962.3|	301291	.	T	<NON_REF>	.	.	END=304678	GT:DP:GQ:MIN_DP:PL	0:66:99:28:0,922
+gi|448814763|ref|NC_000962.3|	304679	.	G	T,<NON_REF>	3530	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3560,0,3560:0,0,46,55
+gi|448814763|ref|NC_000962.3|	304680	.	C	<NON_REF>	.	.	END=304922	GT:DP:GQ:MIN_DP:PL	0:83:99:58:0,1800
+gi|448814763|ref|NC_000962.3|	304923	.	A	G,<NON_REF>	3082	.	DP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,84,0:84:99:3112,0,3112:0,0,52,32
+gi|448814763|ref|NC_000962.3|	304924	.	A	<NON_REF>	.	.	END=310972	GT:DP:GQ:MIN_DP:PL	0:59:99:4:0,135
+gi|448814763|ref|NC_000962.3|	310973	.	G	A,<NON_REF>	1535	.	DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,45,0:45:99:1565,0,1565:0,0,28,17
+gi|448814763|ref|NC_000962.3|	310974	.	C	<NON_REF>	.	.	END=311612	GT:DP:GQ:MIN_DP:PL	0:65:99:42:0,1386
+gi|448814763|ref|NC_000962.3|	311613	.	G	T,<NON_REF>	2695	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2725,0,2725:0,0,44,33
+gi|448814763|ref|NC_000962.3|	311614	.	A	<NON_REF>	.	.	END=315501	GT:DP:GQ:MIN_DP:PL	0:57:99:14:0,405
+gi|448814763|ref|NC_000962.3|	315502	.	C	A,<NON_REF>	1010	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1040,0,1040:0,0,14,16
+gi|448814763|ref|NC_000962.3|	315503	.	C	<NON_REF>	.	.	END=320037	GT:DP:GQ:MIN_DP:PL	0:46:99:13:0,360
+gi|448814763|ref|NC_000962.3|	320038	.	G	A,<NON_REF>	626	.	DP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,19,0:19:99:656,0,656:0,0,9,10
+gi|448814763|ref|NC_000962.3|	320039	.	G	<NON_REF>	.	.	END=328640	GT:DP:GQ:MIN_DP:PL	0:55:99:16:0,484
+gi|448814763|ref|NC_000962.3|	328641	.	G	T,<NON_REF>	1816	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,51,0:51:99:1846,0,1846:0,0,17,34
+gi|448814763|ref|NC_000962.3|	328642	.	G	<NON_REF>	.	.	END=333584	GT:DP:GQ:MIN_DP:PL	0:63:99:4:0,135
+gi|448814763|ref|NC_000962.3|	333585	.	C	<NON_REF>	.	.	END=333588	GT:DP:GQ:MIN_DP:PL	0:6:44:5:0,45
+gi|448814763|ref|NC_000962.3|	333589	.	G	<NON_REF>	.	.	END=333589	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
+gi|448814763|ref|NC_000962.3|	333590	.	C	<NON_REF>	.	.	END=333636	GT:DP:GQ:MIN_DP:PL	0:9:99:7:0,135
+gi|448814763|ref|NC_000962.3|	333637	.	A	<NON_REF>	.	.	END=333637	GT:DP:GQ:MIN_DP:PL	0:9:0:9:0,0
+gi|448814763|ref|NC_000962.3|	333638	.	C	<NON_REF>	.	.	END=333639	GT:DP:GQ:MIN_DP:PL	0:10:99:9:0,315
+gi|448814763|ref|NC_000962.3|	333640	.	G	<NON_REF>	.	.	END=333640	GT:DP:GQ:MIN_DP:PL	0:10:0:10:0,0
+gi|448814763|ref|NC_000962.3|	333641	.	C	<NON_REF>	.	.	END=333641	GT:DP:GQ:MIN_DP:PL	0:10:9:10:0,9
+gi|448814763|ref|NC_000962.3|	333642	.	T	<NON_REF>	.	.	END=333692	GT:DP:GQ:MIN_DP:PL	0:18:99:11:0,180
+gi|448814763|ref|NC_000962.3|	333693	.	C	<NON_REF>	.	.	END=333707	GT:DP:GQ:MIN_DP:PL	0:5:89:2:0,81
+gi|448814763|ref|NC_000962.3|	333708	.	T	<NON_REF>	.	.	END=333708	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
+gi|448814763|ref|NC_000962.3|	333709	.	G	<NON_REF>	.	.	END=333712	GT:DP:GQ:MIN_DP:PL	0:2:83:2:0,83
+gi|448814763|ref|NC_000962.3|	333713	.	A	<NON_REF>	.	.	END=333714	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,71
+gi|448814763|ref|NC_000962.3|	333715	.	C	<NON_REF>	.	.	END=333716	GT:DP:GQ:MIN_DP:PL	0:2:83:2:0,82
+gi|448814763|ref|NC_000962.3|	333717	.	T	<NON_REF>	.	.	END=333750	GT:DP:GQ:MIN_DP:PL	0:7:99:3:0,112
+gi|448814763|ref|NC_000962.3|	333751	.	C	<NON_REF>	.	.	END=333756	GT:DP:GQ:MIN_DP:PL	0:7:89:7:0,90
+gi|448814763|ref|NC_000962.3|	333757	.	C	<NON_REF>	.	.	END=333758	GT:DP:GQ:MIN_DP:PL	0:6:0:5:0,0
+gi|448814763|ref|NC_000962.3|	333759	.	C	<NON_REF>	.	.	END=333766	GT:DP:GQ:MIN_DP:PL	0:3:44:3:0,45
+gi|448814763|ref|NC_000962.3|	333767	.	G	<NON_REF>	.	.	END=333767	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	333768	.	C	<NON_REF>	.	.	END=333768	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	333769	.	C	<NON_REF>	.	.	END=333769	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	333770	.	G	<NON_REF>	.	.	END=333770	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	333771	.	G	<NON_REF>	.	.	END=333776	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	333777	.	C	<NON_REF>	.	.	END=333786	GT:DP:GQ:MIN_DP:PL	0:6:99:4:0,114
+gi|448814763|ref|NC_000962.3|	333787	.	C	<NON_REF>	.	.	END=333787	GT:DP:GQ:MIN_DP:PL	0:7:96:7:0,96
+gi|448814763|ref|NC_000962.3|	333788	.	G	<NON_REF>	.	.	END=333869	GT:DP:GQ:MIN_DP:PL	0:9:99:5:0,135
+gi|448814763|ref|NC_000962.3|	333870	.	C	<NON_REF>	.	.	END=333883	GT:DP:GQ:MIN_DP:PL	0:3:0:3:0,0
+gi|448814763|ref|NC_000962.3|	333884	.	G	<NON_REF>	.	.	END=333890	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	333891	.	C	<NON_REF>	.	.	END=333891	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	333892	.	G	<NON_REF>	.	.	END=333892	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	333893	.	G	<NON_REF>	.	.	END=333893	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	333894	.	A	<NON_REF>	.	.	END=333896	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	333897	.	C	<NON_REF>	.	.	END=333899	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	333900	.	A	<NON_REF>	.	.	END=333900	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	333901	.	A	<NON_REF>	.	.	END=333902	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	333903	.	A	<NON_REF>	.	.	END=333903	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	333904	.	G	<NON_REF>	.	.	END=333923	GT:DP:GQ:MIN_DP:PL	0:1:0:0:0,0
+gi|448814763|ref|NC_000962.3|	333924	.	G	<NON_REF>	.	.	END=333924	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	333925	.	T	<NON_REF>	.	.	END=333926	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	333927	.	C	<NON_REF>	.	.	END=333927	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	333928	.	C	<NON_REF>	.	.	END=333928	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	333929	.	G	<NON_REF>	.	.	END=333929	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,80
+gi|448814763|ref|NC_000962.3|	333930	.	C	<NON_REF>	.	.	END=333931	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	333932	.	G	<NON_REF>	.	.	END=334091	GT:DP:GQ:MIN_DP:PL	0:9:99:3:0,102
+gi|448814763|ref|NC_000962.3|	334092	.	C	<NON_REF>	.	.	END=334093	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	334094	.	G	<NON_REF>	.	.	END=334096	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,131
+gi|448814763|ref|NC_000962.3|	334097	.	G	<NON_REF>	.	.	END=334102	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	334103	.	G	<NON_REF>	.	.	END=334104	GT:DP:GQ:MIN_DP:PL	0:5:99:5:0,135
+gi|448814763|ref|NC_000962.3|	334105	.	C	<NON_REF>	.	.	END=334105	GT:DP:GQ:MIN_DP:PL	0:5:92:5:0,92
+gi|448814763|ref|NC_000962.3|	334106	.	G	<NON_REF>	.	.	END=334108	GT:DP:GQ:MIN_DP:PL	0:5:99:5:0,135
+gi|448814763|ref|NC_000962.3|	334109	.	C	<NON_REF>	.	.	END=334110	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
+gi|448814763|ref|NC_000962.3|	334111	.	C	<NON_REF>	.	.	END=334163	GT:DP:GQ:MIN_DP:PL	0:5:99:3:0,107
+gi|448814763|ref|NC_000962.3|	334164	.	C	<NON_REF>	.	.	END=334166	GT:DP:GQ:MIN_DP:PL	0:6:44:6:0,45
+gi|448814763|ref|NC_000962.3|	334167	.	C	<NON_REF>	.	.	END=334172	GT:DP:GQ:MIN_DP:PL	0:7:89:7:0,90
+gi|448814763|ref|NC_000962.3|	334173	.	C	<NON_REF>	.	.	END=334261	GT:DP:GQ:MIN_DP:PL	0:12:99:4:0,105
+gi|448814763|ref|NC_000962.3|	334262	.	G	<NON_REF>	.	.	END=334262	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	334263	.	C	<NON_REF>	.	.	END=334284	GT:DP:GQ:MIN_DP:PL	0:5:99:3:0,121
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+gi|448814763|ref|NC_000962.3|	336917	.	G	<NON_REF>	.	.	END=336966	GT:DP:GQ:MIN_DP:PL	0:4:99:3:0,117
+gi|448814763|ref|NC_000962.3|	336967	.	T	<NON_REF>	.	.	END=336971	GT:DP:GQ:MIN_DP:PL	0:4:44:4:0,45
+gi|448814763|ref|NC_000962.3|	336972	.	C	<NON_REF>	.	.	END=336983	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	336984	.	A	<NON_REF>	.	.	END=336984	GT:DP:GQ:MIN_DP:PL	0:2:41:2:0,41
+gi|448814763|ref|NC_000962.3|	336985	.	A	<NON_REF>	.	.	END=336985	GT:DP:GQ:MIN_DP:PL	0:2:73:2:0,74
+gi|448814763|ref|NC_000962.3|	336986	.	G	<NON_REF>	.	.	END=336986	GT:DP:GQ:MIN_DP:PL	0:2:64:2:0,64
+gi|448814763|ref|NC_000962.3|	336987	.	G	<NON_REF>	.	.	END=337001	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	337002	.	C	<NON_REF>	.	.	END=337006	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
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+gi|448814763|ref|NC_000962.3|	337008	.	G	<NON_REF>	.	.	END=337008	GT:DP:GQ:MIN_DP:PL	0:2:71:2:0,72
+gi|448814763|ref|NC_000962.3|	337009	.	C	<NON_REF>	.	.	END=337009	GT:DP:GQ:MIN_DP:PL	0:2:82:2:0,83
+gi|448814763|ref|NC_000962.3|	337010	.	A	<NON_REF>	.	.	END=337010	GT:DP:GQ:MIN_DP:PL	0:2:62:2:0,63
+gi|448814763|ref|NC_000962.3|	337011	.	C	<NON_REF>	.	.	END=337015	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,81
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+gi|448814763|ref|NC_000962.3|	337017	.	G	<NON_REF>	.	.	END=337018	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,106
+gi|448814763|ref|NC_000962.3|	337019	.	G	<NON_REF>	.	.	END=337019	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337020	.	C	<NON_REF>	.	.	END=337044	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,126
+gi|448814763|ref|NC_000962.3|	337045	.	G	<NON_REF>	.	.	END=337045	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	337046	.	C	<NON_REF>	.	.	END=337048	GT:DP:GQ:MIN_DP:PL	0:6:99:5:0,135
+gi|448814763|ref|NC_000962.3|	337049	.	C	<NON_REF>	.	.	END=337059	GT:DP:GQ:MIN_DP:PL	0:6:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337060	.	C	<NON_REF>	.	.	END=337060	GT:DP:GQ:MIN_DP:PL	0:2:55:2:0,55
+gi|448814763|ref|NC_000962.3|	337061	.	G	<NON_REF>	.	.	END=337061	GT:DP:GQ:MIN_DP:PL	0:2:58:2:0,58
+gi|448814763|ref|NC_000962.3|	337062	.	T	<NON_REF>	.	.	END=337062	GT:DP:GQ:MIN_DP:PL	0:2:49:2:0,49
+gi|448814763|ref|NC_000962.3|	337063	.	C	<NON_REF>	.	.	END=337063	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	337064	.	G	<NON_REF>	.	.	END=337064	GT:DP:GQ:MIN_DP:PL	0:2:68:2:0,69
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+gi|448814763|ref|NC_000962.3|	337796	.	G	<NON_REF>	.	.	END=337796	GT:DP:GQ:MIN_DP:PL	0:2:55:2:0,55
+gi|448814763|ref|NC_000962.3|	337797	.	C	<NON_REF>	.	.	END=337797	GT:DP:GQ:MIN_DP:PL	0:2:70:2:0,71
+gi|448814763|ref|NC_000962.3|	337798	.	T	<NON_REF>	.	.	END=337798	GT:DP:GQ:MIN_DP:PL	0:2:65:2:0,66
+gi|448814763|ref|NC_000962.3|	337799	.	T	<NON_REF>	.	.	END=337799	GT:DP:GQ:MIN_DP:PL	0:2:53:2:0,53
+gi|448814763|ref|NC_000962.3|	337800	.	C	<NON_REF>	.	.	END=337816	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0
+gi|448814763|ref|NC_000962.3|	337817	.	G	<NON_REF>	.	.	END=337817	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337818	.	G	<NON_REF>	.	.	END=337824	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337825	.	C	<NON_REF>	.	.	END=337828	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337829	.	G	<NON_REF>	.	.	END=337829	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	337830	.	T	<NON_REF>	.	.	END=337830	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337831	.	T	<NON_REF>	.	.	END=337831	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	337832	.	C	<NON_REF>	.	.	END=337833	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337834	.	C	<NON_REF>	.	.	END=337834	GT:DP:GQ:MIN_DP:PL	0:1:42:1:0,43
+gi|448814763|ref|NC_000962.3|	337835	.	G	<NON_REF>	.	.	END=337835	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337836	.	C	<NON_REF>	.	.	END=337836	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337837	.	T	<NON_REF>	.	.	END=337837	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337838	.	G	<NON_REF>	.	.	END=337838	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	337839	.	G	<NON_REF>	.	.	END=337839	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337840	.	C	<NON_REF>	.	.	END=337840	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	337841	.	G	<NON_REF>	.	.	END=337844	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337845	.	C	<NON_REF>	.	.	END=337845	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337846	.	C	<NON_REF>	.	.	END=337846	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337847	.	G	<NON_REF>	.	.	END=337847	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337848	.	T	<NON_REF>	.	.	END=337848	GT:DP:GQ:MIN_DP:PL	0:2:70:2:0,71
+gi|448814763|ref|NC_000962.3|	337849	.	T	<NON_REF>	.	.	END=337850	GT:DP:GQ:MIN_DP:PL	0:2:67:2:0,64
+gi|448814763|ref|NC_000962.3|	337851	.	C	<NON_REF>	.	.	END=337904	GT:DP:GQ:MIN_DP:PL	0:6:99:3:0,119
+gi|448814763|ref|NC_000962.3|	337905	.	C	<NON_REF>	.	.	END=337916	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337917	.	G	<NON_REF>	.	.	END=337917	GT:DP:GQ:MIN_DP:PL	0:2:77:2:0,78
+gi|448814763|ref|NC_000962.3|	337918	.	C	<NON_REF>	.	.	END=337930	GT:DP:GQ:MIN_DP:PL	0:3:89:2:0,82
+gi|448814763|ref|NC_000962.3|	337931	.	G	<NON_REF>	.	.	END=337931	GT:DP:GQ:MIN_DP:PL	0:2:69:2:0,70
+gi|448814763|ref|NC_000962.3|	337932	.	C	<NON_REF>	.	.	END=337934	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,73
+gi|448814763|ref|NC_000962.3|	337935	.	G	<NON_REF>	.	.	END=337935	GT:DP:GQ:MIN_DP:PL	0:2:80:2:0,81
+gi|448814763|ref|NC_000962.3|	337936	.	C	<NON_REF>	.	.	END=337937	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,78
+gi|448814763|ref|NC_000962.3|	337938	.	C	<NON_REF>	.	.	END=337950	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	337951	.	C	<NON_REF>	.	.	END=337951	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337952	.	C	<NON_REF>	.	.	END=337953	GT:DP:GQ:MIN_DP:PL	0:3:78:2:0,76
+gi|448814763|ref|NC_000962.3|	337954	.	C	<NON_REF>	.	.	END=337957	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,101
+gi|448814763|ref|NC_000962.3|	337958	.	G	<NON_REF>	.	.	END=337958	GT:DP:GQ:MIN_DP:PL	0:3:61:3:0,62
+gi|448814763|ref|NC_000962.3|	337959	.	A	<NON_REF>	.	.	END=337959	GT:DP:GQ:MIN_DP:PL	0:3:0:3:0,0
+gi|448814763|ref|NC_000962.3|	337960	.	T	<NON_REF>	.	.	END=337960	GT:DP:GQ:MIN_DP:PL	0:3:82:3:0,82
+gi|448814763|ref|NC_000962.3|	337961	.	G	<NON_REF>	.	.	END=337961	GT:DP:GQ:MIN_DP:PL	0:3:90:3:0,90
+gi|448814763|ref|NC_000962.3|	337962	.	A	<NON_REF>	.	.	END=337962	GT:DP:GQ:MIN_DP:PL	0:3:60:3:0,61
+gi|448814763|ref|NC_000962.3|	337963	.	G	<NON_REF>	.	.	END=337963	GT:DP:GQ:MIN_DP:PL	0:3:90:3:0,90
+gi|448814763|ref|NC_000962.3|	337964	.	C	<NON_REF>	.	.	END=337964	GT:DP:GQ:MIN_DP:PL	0:3:79:3:0,79
+gi|448814763|ref|NC_000962.3|	337965	.	A	<NON_REF>	.	.	END=337965	GT:DP:GQ:MIN_DP:PL	0:3:91:3:0,91
+gi|448814763|ref|NC_000962.3|	337966	.	G	<NON_REF>	.	.	END=337966	GT:DP:GQ:MIN_DP:PL	0:3:77:3:0,78
+gi|448814763|ref|NC_000962.3|	337967	.	A	<NON_REF>	.	.	END=337979	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,111
+gi|448814763|ref|NC_000962.3|	337980	.	C	<NON_REF>	.	.	END=337985	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	337986	.	C	<NON_REF>	.	.	END=337986	GT:DP:GQ:MIN_DP:PL	0:4:44:4:0,45
+gi|448814763|ref|NC_000962.3|	337987	.	C	<NON_REF>	.	.	END=337996	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337997	.	G	<NON_REF>	.	.	END=337997	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
+gi|448814763|ref|NC_000962.3|	337998	.	C	<NON_REF>	.	.	END=337998	GT:DP:GQ:MIN_DP:PL	0:2:80:2:0,81
+gi|448814763|ref|NC_000962.3|	337999	.	C	<NON_REF>	.	.	END=337999	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,79
+gi|448814763|ref|NC_000962.3|	338000	.	G	<NON_REF>	.	.	END=338000	GT:DP:GQ:MIN_DP:PL	0:2:68:2:0,69
+gi|448814763|ref|NC_000962.3|	338001	.	G	<NON_REF>	.	.	END=338003	GT:DP:GQ:MIN_DP:PL	0:2:82:2:0,82
+gi|448814763|ref|NC_000962.3|	338004	.	T	<NON_REF>	.	.	END=338005	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,73
+gi|448814763|ref|NC_000962.3|	338006	.	G	<NON_REF>	.	.	END=338006	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	338007	.	A	<NON_REF>	.	.	END=338008	GT:DP:GQ:MIN_DP:PL	0:2:74:2:0,75
+gi|448814763|ref|NC_000962.3|	338009	.	G	<NON_REF>	.	.	END=338012	GT:DP:GQ:MIN_DP:PL	0:2:82:2:0,83
+gi|448814763|ref|NC_000962.3|	338013	.	A	<NON_REF>	.	.	END=338014	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,76
+gi|448814763|ref|NC_000962.3|	338015	.	C	<NON_REF>	.	.	END=338015	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	338016	.	C	<NON_REF>	.	.	END=338019	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338020	.	A	C,<NON_REF>	45	.	DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,2,0:2:75:75,0,75:0,0,2,0
+gi|448814763|ref|NC_000962.3|	338021	.	G	<NON_REF>	.	.	END=338022	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338023	.	C	<NON_REF>	.	.	END=338029	GT:DP:GQ:MIN_DP:PL	0:2:0:2:0,0
+gi|448814763|ref|NC_000962.3|	338030	.	G	<NON_REF>	.	.	END=338038	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338039	.	G	<NON_REF>	.	.	END=338039	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	338040	.	G	<NON_REF>	.	.	END=338040	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	338041	.	A	<NON_REF>	.	.	END=338041	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	338042	.	G	<NON_REF>	.	.	END=338042	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	338043	.	C	<NON_REF>	.	.	END=338044	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	338045	.	G	<NON_REF>	.	.	END=338045	GT:DP:GQ:MIN_DP:PL	0:2:73:2:0,74
+gi|448814763|ref|NC_000962.3|	338046	.	A	<NON_REF>	.	.	END=338099	GT:DP:GQ:MIN_DP:PL	0:8:99:3:0,102
+gi|448814763|ref|NC_000962.3|	338100	.	T	C,<NON_REF>	216	.	DP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,6,0:6:99:246,0,246:0,0,6,0
+gi|448814763|ref|NC_000962.3|	338101	.	T	<NON_REF>	.	.	END=338166	GT:DP:GQ:MIN_DP:PL	0:7:99:5:0,135
+gi|448814763|ref|NC_000962.3|	338167	.	C	<NON_REF>	.	.	END=338177	GT:DP:GQ:MIN_DP:PL	0:3:0:3:0,0
+gi|448814763|ref|NC_000962.3|	338178	.	C	<NON_REF>	.	.	END=338179	GT:DP:GQ:MIN_DP:PL	0:4:44:3:0,45
+gi|448814763|ref|NC_000962.3|	338180	.	G	<NON_REF>	.	.	END=338181	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	338182	.	C	<NON_REF>	.	.	END=338183	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	338184	.	A	<NON_REF>	.	.	END=338184	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	338185	.	C	<NON_REF>	.	.	END=338185	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	338186	.	G	<NON_REF>	.	.	END=338186	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	338187	.	T	<NON_REF>	.	.	END=338187	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	338188	.	T	<NON_REF>	.	.	END=338188	GT:DP:GQ:MIN_DP:PL	0:1:33:1:0,34
+gi|448814763|ref|NC_000962.3|	338189	.	G	<NON_REF>	.	.	END=338189	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	338190	.	A	<NON_REF>	.	.	END=338190	GT:DP:GQ:MIN_DP:PL	0:1:37:1:0,38
+gi|448814763|ref|NC_000962.3|	338191	.	T	<NON_REF>	.	.	END=338192	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	338193	.	A	<NON_REF>	.	.	END=338193	GT:DP:GQ:MIN_DP:PL	0:1:38:1:0,39
+gi|448814763|ref|NC_000962.3|	338194	.	T	<NON_REF>	.	.	END=338194	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	338195	.	G	<NON_REF>	.	.	END=338196	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	338197	.	T	<NON_REF>	.	.	END=338197	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	338198	.	C	<NON_REF>	.	.	END=338199	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	338200	.	T	<NON_REF>	.	.	END=338200	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	338201	.	C	<NON_REF>	.	.	END=338201	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	338202	.	C	<NON_REF>	.	.	END=338202	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	338203	.	C	<NON_REF>	.	.	END=338203	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
+gi|448814763|ref|NC_000962.3|	338204	.	G	<NON_REF>	.	.	END=338204	GT:DP:GQ:MIN_DP:PL	0:2:77:2:0,78
+gi|448814763|ref|NC_000962.3|	338205	.	C	<NON_REF>	.	.	END=338206	GT:DP:GQ:MIN_DP:PL	0:2:80:2:0,81
+gi|448814763|ref|NC_000962.3|	338207	.	A	<NON_REF>	.	.	END=338207	GT:DP:GQ:MIN_DP:PL	0:2:77:2:0,78
+gi|448814763|ref|NC_000962.3|	338208	.	C	<NON_REF>	.	.	END=338379	GT:DP:GQ:MIN_DP:PL	0:8:99:3:0,108
+gi|448814763|ref|NC_000962.3|	338380	.	C	<NON_REF>	.	.	END=338388	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	338389	.	C	<NON_REF>	.	.	END=338389	GT:DP:GQ:MIN_DP:PL	0:4:44:4:0,45
+gi|448814763|ref|NC_000962.3|	338390	.	C	<NON_REF>	.	.	END=338396	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	338397	.	T	<NON_REF>	.	.	END=338400	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338401	.	C	<NON_REF>	.	.	END=338401	GT:DP:GQ:MIN_DP:PL	0:2:3:2:0,3
+gi|448814763|ref|NC_000962.3|	338402	.	G	<NON_REF>	.	.	END=338402	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338403	.	A	<NON_REF>	.	.	END=338406	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	338407	.	G	<NON_REF>	.	.	END=338407	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
+gi|448814763|ref|NC_000962.3|	338408	.	C	<NON_REF>	.	.	END=338408	GT:DP:GQ:MIN_DP:PL	0:2:3:2:0,3
+gi|448814763|ref|NC_000962.3|	338409	.	C	<NON_REF>	.	.	END=338413	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,81
+gi|448814763|ref|NC_000962.3|	338414	.	G	<NON_REF>	.	.	END=338414	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,79
+gi|448814763|ref|NC_000962.3|	338415	.	T	<NON_REF>	.	.	END=338415	GT:DP:GQ:MIN_DP:PL	0:2:65:2:0,66
+gi|448814763|ref|NC_000962.3|	338416	.	T	<NON_REF>	.	.	END=338416	GT:DP:GQ:MIN_DP:PL	0:2:73:2:0,74
+gi|448814763|ref|NC_000962.3|	338417	.	T	<NON_REF>	.	.	END=338417	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338418	.	C	<NON_REF>	.	.	END=338422	GT:DP:GQ:MIN_DP:PL	0:2:0:2:0,0
+gi|448814763|ref|NC_000962.3|	338423	.	G	<NON_REF>	.	.	END=338425	GT:DP:GQ:MIN_DP:PL	0:3:44:3:0,45
+gi|448814763|ref|NC_000962.3|	338426	.	C	<NON_REF>	.	.	END=338426	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	338427	.	C	<NON_REF>	.	.	END=338434	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,130
+gi|448814763|ref|NC_000962.3|	338435	.	G	<NON_REF>	.	.	END=338435	GT:DP:GQ:MIN_DP:PL	0:4:41:4:0,41
+gi|448814763|ref|NC_000962.3|	338436	.	C	<NON_REF>	.	.	END=338452	GT:DP:GQ:MIN_DP:PL	0:7:99:6:0,195
diff -r 000000000000 -r bf8841b0a6b0 test-data/nonvariants_output1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nonvariants_output1.vcf	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,884 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 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=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 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=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false 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 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null 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">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive)
+##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive)
+##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive)
+##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive)
+##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive)
+##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive)
+##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive)
+##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive)
+##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive)
+##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive)
+##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive)
+##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive)
+##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive)
+##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive)
+##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive)
+##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive)
+##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
+##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##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=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=gi|448814763|ref|NC_000962.3|,length=4411532>
+##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	./R_2117_866#L5-_.R
+gi|448814763|ref|NC_000962.3|	1	.	T	<NON_REF>	.	.	END=1976	GT:DP:GQ:MIN_DP:PL	0:97:99:51:0,1710
+gi|448814763|ref|NC_000962.3|	1978	.	T	<NON_REF>	.	.	END=4012	GT:DP:GQ:MIN_DP:PL	0:90:99:52:0,1779
+gi|448814763|ref|NC_000962.3|	4014	.	C	<NON_REF>	.	.	END=7361	GT:DP:GQ:MIN_DP:PL	0:70:99:35:0,1159
+gi|448814763|ref|NC_000962.3|	7363	.	A	<NON_REF>	.	.	END=7584	GT:DP:GQ:MIN_DP:PL	0:60:99:50:0,1746
+gi|448814763|ref|NC_000962.3|	7586	.	C	<NON_REF>	.	.	END=9303	GT:DP:GQ:MIN_DP:PL	0:76:99:46:0,1601
+gi|448814763|ref|NC_000962.3|	9305	.	C	<NON_REF>	.	.	END=11310	GT:DP:GQ:MIN_DP:PL	0:69:99:19:0,644
+gi|448814763|ref|NC_000962.3|	11312	.	G	<NON_REF>	.	.	END=11369	GT:DP:GQ:MIN_DP:PL	0:83:99:78:0,1800
+gi|448814763|ref|NC_000962.3|	11371	.	C	<NON_REF>	.	.	END=11878	GT:DP:GQ:MIN_DP:PL	0:71:99:40:0,1215
+gi|448814763|ref|NC_000962.3|	11880	.	G	<NON_REF>	.	.	END=14784	GT:DP:GQ:MIN_DP:PL	0:71:99:27:0,765
+gi|448814763|ref|NC_000962.3|	14786	.	G	<NON_REF>	.	.	END=21794	GT:DP:GQ:MIN_DP:PL	0:70:99:15:0,405
+gi|448814763|ref|NC_000962.3|	21796	.	C	<NON_REF>	.	.	END=24697	GT:DP:GQ:MIN_DP:PL	0:60:99:5:0,135
+gi|448814763|ref|NC_000962.3|	24717	.	C	<NON_REF>	.	.	END=24717	GT:DP:GQ:MIN_DP:PL	0:38:0:38:0,0
+gi|448814763|ref|NC_000962.3|	24718	.	C	<NON_REF>	.	.	END=26958	GT:DP:GQ:MIN_DP:PL	0:60:99:26:0,852
+gi|448814763|ref|NC_000962.3|	26960	.	C	<NON_REF>	.	.	END=29474	GT:DP:GQ:MIN_DP:PL	0:54:99:21:0,405
+gi|448814763|ref|NC_000962.3|	29475	.	T	<NON_REF>	.	.	END=29476	GT:DP:GQ:MIN_DP:PL	0:70:44:69:0,45
+gi|448814763|ref|NC_000962.3|	29477	.	A	<NON_REF>	.	.	END=29480	GT:DP:GQ:MIN_DP:PL	0:72:0:71:0,0
+gi|448814763|ref|NC_000962.3|	29481	.	T	<NON_REF>	.	.	END=29481	GT:DP:GQ:MIN_DP:PL	0:72:44:72:0,45
+gi|448814763|ref|NC_000962.3|	29484	.	A	<NON_REF>	.	.	END=29484	GT:DP:GQ:MIN_DP:PL	0:74:0:74:0,0
+gi|448814763|ref|NC_000962.3|	29485	.	A	<NON_REF>	.	.	END=30518	GT:DP:GQ:MIN_DP:PL	0:78:99:26:0,798
+gi|448814763|ref|NC_000962.3|	30520	.	G	<NON_REF>	.	.	END=30687	GT:DP:GQ:MIN_DP:PL	0:66:99:54:0,1653
+gi|448814763|ref|NC_000962.3|	30689	.	C	<NON_REF>	.	.	END=30942	GT:DP:GQ:MIN_DP:PL	0:49:99:29:0,959
+gi|448814763|ref|NC_000962.3|	30944	.	C	<NON_REF>	.	.	END=31076	GT:DP:GQ:MIN_DP:PL	0:58:99:43:0,1528
+gi|448814763|ref|NC_000962.3|	31078	.	A	<NON_REF>	.	.	END=32341	GT:DP:GQ:MIN_DP:PL	0:69:99:39:0,135
+gi|448814763|ref|NC_000962.3|	32342	.	G	<NON_REF>	.	.	END=32348	GT:DP:GQ:MIN_DP:PL	0:41:0:41:0,0
+gi|448814763|ref|NC_000962.3|	32387	.	C	<NON_REF>	.	.	END=34043	GT:DP:GQ:MIN_DP:PL	0:60:99:26:0,900
+gi|448814763|ref|NC_000962.3|	34045	.	G	<NON_REF>	.	.	END=37030	GT:DP:GQ:MIN_DP:PL	0:89:99:30:0,900
+gi|448814763|ref|NC_000962.3|	37032	.	T	<NON_REF>	.	.	END=37909	GT:DP:GQ:MIN_DP:PL	0:58:99:36:0,1260
+gi|448814763|ref|NC_000962.3|	37911	.	C	<NON_REF>	.	.	END=39218	GT:DP:GQ:MIN_DP:PL	0:65:99:30:0,180
+gi|448814763|ref|NC_000962.3|	39219	.	G	<NON_REF>	.	.	END=39221	GT:DP:GQ:MIN_DP:PL	0:49:0:48:0,0
+gi|448814763|ref|NC_000962.3|	39222	.	G	<NON_REF>	.	.	END=39222	GT:DP:GQ:MIN_DP:PL	0:52:99:52:0,135
+gi|448814763|ref|NC_000962.3|	39225	.	C	<NON_REF>	.	.	END=39225	GT:DP:GQ:MIN_DP:PL	0:49:0:49:0,0
+gi|448814763|ref|NC_000962.3|	39226	.	C	<NON_REF>	.	.	END=42966	GT:DP:GQ:MIN_DP:PL	0:46:99:20:0,633
+gi|448814763|ref|NC_000962.3|	42968	.	G	<NON_REF>	.	.	END=50556	GT:DP:GQ:MIN_DP:PL	0:65:99:15:0,315
+gi|448814763|ref|NC_000962.3|	50558	.	G	<NON_REF>	.	.	END=51948	GT:DP:GQ:MIN_DP:PL	0:73:99:39:0,1288
+gi|448814763|ref|NC_000962.3|	51950	.	C	<NON_REF>	.	.	END=51953	GT:DP:GQ:MIN_DP:PL	0:77:99:75:0,1800
+gi|448814763|ref|NC_000962.3|	51955	.	T	<NON_REF>	.	.	END=53784	GT:DP:GQ:MIN_DP:PL	0:57:99:11:0,364
+gi|448814763|ref|NC_000962.3|	53786	.	G	<NON_REF>	.	.	END=54393	GT:DP:GQ:MIN_DP:PL	0:95:99:64:0,1800
+gi|448814763|ref|NC_000962.3|	54395	.	G	<NON_REF>	.	.	END=55533	GT:DP:GQ:MIN_DP:PL	0:72:99:19:0,270
+gi|448814763|ref|NC_000962.3|	55534	.	G	<NON_REF>	.	.	END=55552	GT:DP:GQ:MIN_DP:PL	0:25:0:20:0,0
+gi|448814763|ref|NC_000962.3|	55554	.	C	<NON_REF>	.	.	END=55554	GT:DP:GQ:MIN_DP:PL	0:26:0:26:0,0
+gi|448814763|ref|NC_000962.3|	55555	.	G	<NON_REF>	.	.	END=57392	GT:DP:GQ:MIN_DP:PL	0:48:99:14:0,422
+gi|448814763|ref|NC_000962.3|	57394	.	C	<NON_REF>	.	.	END=62048	GT:DP:GQ:MIN_DP:PL	0:68:99:22:0,720
+gi|448814763|ref|NC_000962.3|	62050	.	G	<NON_REF>	.	.	END=62656	GT:DP:GQ:MIN_DP:PL	0:86:99:37:0,1231
+gi|448814763|ref|NC_000962.3|	62658	.	A	<NON_REF>	.	.	END=66284	GT:DP:GQ:MIN_DP:PL	0:87:99:26:0,900
+gi|448814763|ref|NC_000962.3|	66286	.	G	<NON_REF>	.	.	END=69870	GT:DP:GQ:MIN_DP:PL	0:57:99:17:0,495
+gi|448814763|ref|NC_000962.3|	69872	.	T	<NON_REF>	.	.	END=69988	GT:DP:GQ:MIN_DP:PL	0:69:99:53:0,1800
+gi|448814763|ref|NC_000962.3|	69990	.	T	<NON_REF>	.	.	END=70815	GT:DP:GQ:MIN_DP:PL	0:76:99:36:0,1125
+gi|448814763|ref|NC_000962.3|	70817	.	A	<NON_REF>	.	.	END=71335	GT:DP:GQ:MIN_DP:PL	0:72:99:33:0,900
+gi|448814763|ref|NC_000962.3|	71337	.	C	<NON_REF>	.	.	END=71583	GT:DP:GQ:MIN_DP:PL	0:40:99:8:0,180
+gi|448814763|ref|NC_000962.3|	71585	.	C	<NON_REF>	.	.	END=75263	GT:DP:GQ:MIN_DP:PL	0:78:99:28:0,389
+gi|448814763|ref|NC_000962.3|	75265	.	T	<NON_REF>	.	.	END=75939	GT:DP:GQ:MIN_DP:PL	0:56:99:34:0,1161
+gi|448814763|ref|NC_000962.3|	75941	.	T	<NON_REF>	.	.	END=80615	GT:DP:GQ:MIN_DP:PL	0:65:99:24:0,135
+gi|448814763|ref|NC_000962.3|	80617	.	T	<NON_REF>	.	.	END=83981	GT:DP:GQ:MIN_DP:PL	0:72:99:31:0,1146
+gi|448814763|ref|NC_000962.3|	83983	.	A	<NON_REF>	.	.	END=86575	GT:DP:GQ:MIN_DP:PL	0:67:99:27:0,900
+gi|448814763|ref|NC_000962.3|	86577	.	A	<NON_REF>	.	.	END=92198	GT:DP:GQ:MIN_DP:PL	0:47:99:5:0,135
+gi|448814763|ref|NC_000962.3|	92200	.	C	<NON_REF>	.	.	END=95590	GT:DP:GQ:MIN_DP:PL	0:46:99:20:0,756
+gi|448814763|ref|NC_000962.3|	95592	.	A	<NON_REF>	.	.	END=97387	GT:DP:GQ:MIN_DP:PL	0:62:99:25:0,675
+gi|448814763|ref|NC_000962.3|	97389	.	A	<NON_REF>	.	.	END=103835	GT:DP:GQ:MIN_DP:PL	0:55:99:12:0,423
+gi|448814763|ref|NC_000962.3|	103837	.	T	<NON_REF>	.	.	END=103883	GT:DP:GQ:MIN_DP:PL	0:10:99:8:0,135
+gi|448814763|ref|NC_000962.3|	103884	.	G	<NON_REF>	.	.	END=103888	GT:DP:GQ:MIN_DP:PL	0:5:89:5:0,90
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+gi|448814763|ref|NC_000962.3|	336890	.	G	<NON_REF>	.	.	END=336890	GT:DP:GQ:MIN_DP:PL	0:3:53:3:0,54
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+gi|448814763|ref|NC_000962.3|	336894	.	T	<NON_REF>	.	.	END=336894	GT:DP:GQ:MIN_DP:PL	0:3:37:3:0,38
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+gi|448814763|ref|NC_000962.3|	336967	.	T	<NON_REF>	.	.	END=336971	GT:DP:GQ:MIN_DP:PL	0:4:44:4:0,45
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+gi|448814763|ref|NC_000962.3|	337402	.	T	<NON_REF>	.	.	END=337406	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,106
+gi|448814763|ref|NC_000962.3|	337407	.	C	<NON_REF>	.	.	END=337408	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337409	.	G	<NON_REF>	.	.	END=337726	GT:DP:GQ:MIN_DP:PL	0:14:99:4:0,133
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+gi|448814763|ref|NC_000962.3|	337744	.	G	<NON_REF>	.	.	END=337745	GT:DP:GQ:MIN_DP:PL	0:3:86:3:0,85
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+gi|448814763|ref|NC_000962.3|	337752	.	G	<NON_REF>	.	.	END=337752	GT:DP:GQ:MIN_DP:PL	0:2:61:2:0,61
+gi|448814763|ref|NC_000962.3|	337753	.	T	<NON_REF>	.	.	END=337753	GT:DP:GQ:MIN_DP:PL	0:3:82:3:0,82
+gi|448814763|ref|NC_000962.3|	337754	.	G	<NON_REF>	.	.	END=337754	GT:DP:GQ:MIN_DP:PL	0:3:71:3:0,72
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+gi|448814763|ref|NC_000962.3|	337767	.	C	<NON_REF>	.	.	END=337775	GT:DP:GQ:MIN_DP:PL	0:5:89:4:0,90
+gi|448814763|ref|NC_000962.3|	337776	.	C	<NON_REF>	.	.	END=337785	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,126
+gi|448814763|ref|NC_000962.3|	337786	.	T	<NON_REF>	.	.	END=337795	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337796	.	G	<NON_REF>	.	.	END=337796	GT:DP:GQ:MIN_DP:PL	0:2:55:2:0,55
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+gi|448814763|ref|NC_000962.3|	337798	.	T	<NON_REF>	.	.	END=337798	GT:DP:GQ:MIN_DP:PL	0:2:65:2:0,66
+gi|448814763|ref|NC_000962.3|	337799	.	T	<NON_REF>	.	.	END=337799	GT:DP:GQ:MIN_DP:PL	0:2:53:2:0,53
+gi|448814763|ref|NC_000962.3|	337800	.	C	<NON_REF>	.	.	END=337816	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0
+gi|448814763|ref|NC_000962.3|	337817	.	G	<NON_REF>	.	.	END=337817	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337818	.	G	<NON_REF>	.	.	END=337824	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337825	.	C	<NON_REF>	.	.	END=337828	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337829	.	G	<NON_REF>	.	.	END=337829	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	337830	.	T	<NON_REF>	.	.	END=337830	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337831	.	T	<NON_REF>	.	.	END=337831	GT:DP:GQ:MIN_DP:PL	0:1:35:1:0,36
+gi|448814763|ref|NC_000962.3|	337832	.	C	<NON_REF>	.	.	END=337833	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337834	.	C	<NON_REF>	.	.	END=337834	GT:DP:GQ:MIN_DP:PL	0:1:42:1:0,43
+gi|448814763|ref|NC_000962.3|	337835	.	G	<NON_REF>	.	.	END=337835	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337836	.	C	<NON_REF>	.	.	END=337836	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337837	.	T	<NON_REF>	.	.	END=337837	GT:DP:GQ:MIN_DP:PL	0:1:0:1:0,0
+gi|448814763|ref|NC_000962.3|	337838	.	G	<NON_REF>	.	.	END=337838	GT:DP:GQ:MIN_DP:PL	0:1:41:1:0,42
+gi|448814763|ref|NC_000962.3|	337839	.	G	<NON_REF>	.	.	END=337839	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337840	.	C	<NON_REF>	.	.	END=337840	GT:DP:GQ:MIN_DP:PL	0:1:36:1:0,37
+gi|448814763|ref|NC_000962.3|	337841	.	G	<NON_REF>	.	.	END=337844	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337845	.	C	<NON_REF>	.	.	END=337845	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337846	.	C	<NON_REF>	.	.	END=337846	GT:DP:GQ:MIN_DP:PL	0:1:40:1:0,41
+gi|448814763|ref|NC_000962.3|	337847	.	G	<NON_REF>	.	.	END=337847	GT:DP:GQ:MIN_DP:PL	0:1:39:1:0,40
+gi|448814763|ref|NC_000962.3|	337848	.	T	<NON_REF>	.	.	END=337848	GT:DP:GQ:MIN_DP:PL	0:2:70:2:0,71
+gi|448814763|ref|NC_000962.3|	337849	.	T	<NON_REF>	.	.	END=337850	GT:DP:GQ:MIN_DP:PL	0:2:67:2:0,64
+gi|448814763|ref|NC_000962.3|	337851	.	C	<NON_REF>	.	.	END=337904	GT:DP:GQ:MIN_DP:PL	0:6:99:3:0,119
+gi|448814763|ref|NC_000962.3|	337905	.	C	<NON_REF>	.	.	END=337916	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337917	.	G	<NON_REF>	.	.	END=337917	GT:DP:GQ:MIN_DP:PL	0:2:77:2:0,78
+gi|448814763|ref|NC_000962.3|	337918	.	C	<NON_REF>	.	.	END=337930	GT:DP:GQ:MIN_DP:PL	0:3:89:2:0,82
+gi|448814763|ref|NC_000962.3|	337931	.	G	<NON_REF>	.	.	END=337931	GT:DP:GQ:MIN_DP:PL	0:2:69:2:0,70
+gi|448814763|ref|NC_000962.3|	337932	.	C	<NON_REF>	.	.	END=337934	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,73
+gi|448814763|ref|NC_000962.3|	337935	.	G	<NON_REF>	.	.	END=337935	GT:DP:GQ:MIN_DP:PL	0:2:80:2:0,81
+gi|448814763|ref|NC_000962.3|	337936	.	C	<NON_REF>	.	.	END=337937	GT:DP:GQ:MIN_DP:PL	0:2:79:2:0,78
+gi|448814763|ref|NC_000962.3|	337938	.	C	<NON_REF>	.	.	END=337950	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
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+gi|448814763|ref|NC_000962.3|	337952	.	C	<NON_REF>	.	.	END=337953	GT:DP:GQ:MIN_DP:PL	0:3:78:2:0,76
+gi|448814763|ref|NC_000962.3|	337954	.	C	<NON_REF>	.	.	END=337957	GT:DP:GQ:MIN_DP:PL	0:3:99:3:0,101
+gi|448814763|ref|NC_000962.3|	337958	.	G	<NON_REF>	.	.	END=337958	GT:DP:GQ:MIN_DP:PL	0:3:61:3:0,62
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+gi|448814763|ref|NC_000962.3|	337960	.	T	<NON_REF>	.	.	END=337960	GT:DP:GQ:MIN_DP:PL	0:3:82:3:0,82
+gi|448814763|ref|NC_000962.3|	337961	.	G	<NON_REF>	.	.	END=337961	GT:DP:GQ:MIN_DP:PL	0:3:90:3:0,90
+gi|448814763|ref|NC_000962.3|	337962	.	A	<NON_REF>	.	.	END=337962	GT:DP:GQ:MIN_DP:PL	0:3:60:3:0,61
+gi|448814763|ref|NC_000962.3|	337963	.	G	<NON_REF>	.	.	END=337963	GT:DP:GQ:MIN_DP:PL	0:3:90:3:0,90
+gi|448814763|ref|NC_000962.3|	337964	.	C	<NON_REF>	.	.	END=337964	GT:DP:GQ:MIN_DP:PL	0:3:79:3:0,79
+gi|448814763|ref|NC_000962.3|	337965	.	A	<NON_REF>	.	.	END=337965	GT:DP:GQ:MIN_DP:PL	0:3:91:3:0,91
+gi|448814763|ref|NC_000962.3|	337966	.	G	<NON_REF>	.	.	END=337966	GT:DP:GQ:MIN_DP:PL	0:3:77:3:0,78
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+gi|448814763|ref|NC_000962.3|	337986	.	C	<NON_REF>	.	.	END=337986	GT:DP:GQ:MIN_DP:PL	0:4:44:4:0,45
+gi|448814763|ref|NC_000962.3|	337987	.	C	<NON_REF>	.	.	END=337996	GT:DP:GQ:MIN_DP:PL	0:4:89:3:0,90
+gi|448814763|ref|NC_000962.3|	337997	.	G	<NON_REF>	.	.	END=337997	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
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+gi|448814763|ref|NC_000962.3|	338006	.	G	<NON_REF>	.	.	END=338006	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,82
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+gi|448814763|ref|NC_000962.3|	338390	.	C	<NON_REF>	.	.	END=338396	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	338397	.	T	<NON_REF>	.	.	END=338400	GT:DP:GQ:MIN_DP:PL	0:3:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338401	.	C	<NON_REF>	.	.	END=338401	GT:DP:GQ:MIN_DP:PL	0:2:3:2:0,3
+gi|448814763|ref|NC_000962.3|	338402	.	G	<NON_REF>	.	.	END=338402	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338403	.	A	<NON_REF>	.	.	END=338406	GT:DP:GQ:MIN_DP:PL	0:3:89:3:0,90
+gi|448814763|ref|NC_000962.3|	338407	.	G	<NON_REF>	.	.	END=338407	GT:DP:GQ:MIN_DP:PL	0:2:76:2:0,77
+gi|448814763|ref|NC_000962.3|	338408	.	C	<NON_REF>	.	.	END=338408	GT:DP:GQ:MIN_DP:PL	0:2:3:2:0,3
+gi|448814763|ref|NC_000962.3|	338409	.	C	<NON_REF>	.	.	END=338413	GT:DP:GQ:MIN_DP:PL	0:2:81:2:0,81
+gi|448814763|ref|NC_000962.3|	338414	.	G	<NON_REF>	.	.	END=338414	GT:DP:GQ:MIN_DP:PL	0:2:78:2:0,79
+gi|448814763|ref|NC_000962.3|	338415	.	T	<NON_REF>	.	.	END=338415	GT:DP:GQ:MIN_DP:PL	0:2:65:2:0,66
+gi|448814763|ref|NC_000962.3|	338416	.	T	<NON_REF>	.	.	END=338416	GT:DP:GQ:MIN_DP:PL	0:2:73:2:0,74
+gi|448814763|ref|NC_000962.3|	338417	.	T	<NON_REF>	.	.	END=338417	GT:DP:GQ:MIN_DP:PL	0:2:44:2:0,45
+gi|448814763|ref|NC_000962.3|	338418	.	C	<NON_REF>	.	.	END=338422	GT:DP:GQ:MIN_DP:PL	0:2:0:2:0,0
+gi|448814763|ref|NC_000962.3|	338423	.	G	<NON_REF>	.	.	END=338425	GT:DP:GQ:MIN_DP:PL	0:3:44:3:0,45
+gi|448814763|ref|NC_000962.3|	338426	.	C	<NON_REF>	.	.	END=338426	GT:DP:GQ:MIN_DP:PL	0:4:89:4:0,90
+gi|448814763|ref|NC_000962.3|	338427	.	C	<NON_REF>	.	.	END=338434	GT:DP:GQ:MIN_DP:PL	0:4:99:4:0,130
+gi|448814763|ref|NC_000962.3|	338435	.	G	<NON_REF>	.	.	END=338435	GT:DP:GQ:MIN_DP:PL	0:4:41:4:0,41
+gi|448814763|ref|NC_000962.3|	338436	.	C	<NON_REF>	.	.	END=338452	GT:DP:GQ:MIN_DP:PL	0:7:99:6:0,195
diff -r 000000000000 -r bf8841b0a6b0 test-data/variants_noheader_output1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variants_noheader_output1.vcf	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,116 @@
+gi|448814763|ref|NC_000962.3|	1977	.	A	G,<NON_REF>	1986	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2016,0,2016:0,0,11,42
+gi|448814763|ref|NC_000962.3|	4013	.	T	C,<NON_REF>	2081	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2111,0,2111:0,0,29,24
+gi|448814763|ref|NC_000962.3|	7362	.	G	C,<NON_REF>	3369	.	BaseQRankSum=1.693;ClippingRankSum=1.693;DP=88;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=0.827;ReadPosRankSum=1.614	GT:AD:DP:GQ:PL:SB	1:1,87,0:88:99:3399,0,3408:0,1,40,47
+gi|448814763|ref|NC_000962.3|	7585	.	G	C,<NON_REF>	2294	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2324,0,2324:0,0,36,24
+gi|448814763|ref|NC_000962.3|	9304	.	G	A,<NON_REF>	2343	.	DP=69;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2373,0,2373:0,0,31,38
+gi|448814763|ref|NC_000962.3|	11311	.	A	C,<NON_REF>	3627	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3657,0,3657:0,0,31,65
+gi|448814763|ref|NC_000962.3|	11370	.	C	T,<NON_REF>	2699	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2729,0,2729:0,0,21,56
+gi|448814763|ref|NC_000962.3|	11879	.	A	G,<NON_REF>	2659	.	DP=70;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2689,0,2689:0,0,36,33
+gi|448814763|ref|NC_000962.3|	14785	.	T	C,<NON_REF>	3506	.	DP=90;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,90,0:90:99:3536,0,3536:0,0,38,52
+gi|448814763|ref|NC_000962.3|	21795	.	G	A,<NON_REF>	784	.	DP=24;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:814,0,814:0,0,8,16
+gi|448814763|ref|NC_000962.3|	24698	.	GCCGCGTTGCTCGGGGTAA	G,<NON_REF>	1536.97	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.01;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1576,0,1576:0,0,25,11
+gi|448814763|ref|NC_000962.3|	26959	.	C	G,<NON_REF>	2474	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2504,0,2504:0,0,41,25
+gi|448814763|ref|NC_000962.3|	29482	.	CA	C,<NON_REF>	2528.97	.	DP=74;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.14;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2568,0,2568:0,0,34,38
+gi|448814763|ref|NC_000962.3|	30519	.	C	T,<NON_REF>	2289	.	BaseQRankSum=1.681;ClippingRankSum=0.026;DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.525;ReadPosRankSum=1.060	GT:AD:DP:GQ:PL:SB	1:1,66,0:67:99:2319,0,2329:1,0,47,19
+gi|448814763|ref|NC_000962.3|	30688	.	T	G,<NON_REF>	2109	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2139,0,2139:0,0,30,26
+gi|448814763|ref|NC_000962.3|	30943	.	C	T,<NON_REF>	1534	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1564,0,1564:0,0,28,21
+gi|448814763|ref|NC_000962.3|	31077	.	C	T,<NON_REF>	1499	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,43,0:43:99:1529,0,1529:0,0,24,19
+gi|448814763|ref|NC_000962.3|	32349	.	CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG	C,<NON_REF>	3070.97	.	DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=65.20;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,70,0:70:99:3110,0,3110:0,0,35,35
+gi|448814763|ref|NC_000962.3|	34044	.	T	C,<NON_REF>	3703	.	DP=94;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,94,0:94:99:3733,0,3733:0,0,60,34
+gi|448814763|ref|NC_000962.3|	37031	.	C	G,<NON_REF>	1773	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1803,0,1803:0,0,22,24
+gi|448814763|ref|NC_000962.3|	37910	.	C	A,<NON_REF>	3793	.	DP=113;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3823,0,3823:0,0,62,51
+gi|448814763|ref|NC_000962.3|	39223	.	GC	G,<NON_REF>	1460.97	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1500,0,1500:0,0,19,27
+gi|448814763|ref|NC_000962.3|	42967	.	G	C,<NON_REF>	2609	.	DP=67;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,67,0:67:99:2639,0,2639:0,0,15,52
+gi|448814763|ref|NC_000962.3|	50557	.	T	C,<NON_REF>	2896	.	DP=73;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,73,0:73:99:2926,0,2926:0,0,43,30
+gi|448814763|ref|NC_000962.3|	51949	.	A	G,<NON_REF>	3374	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,76,0:76:99:3404,0,3404:0,0,33,43
+gi|448814763|ref|NC_000962.3|	51954	.	T	A,<NON_REF>	3329	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,71,0:71:99:3359,0,3359:0,0,29,42
+gi|448814763|ref|NC_000962.3|	53785	.	C	G,<NON_REF>	3639	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3669,0,3669:0,0,54,42
+gi|448814763|ref|NC_000962.3|	54394	.	A	G,<NON_REF>	3218	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3248,0,3248:0,0,40,43
+gi|448814763|ref|NC_000962.3|	55553	.	C	CCGCCGT,<NON_REF>	942.97	.	DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=74.16;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:982,0,982:0,0,8,16
+gi|448814763|ref|NC_000962.3|	57393	.	A	T,<NON_REF>	1304	.	DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1334,0,1334:0,0,32,4
+gi|448814763|ref|NC_000962.3|	62049	.	A	G,<NON_REF>	1820	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1850,0,1850:0,0,24,24
+gi|448814763|ref|NC_000962.3|	62657	.	G	A,<NON_REF>	3950	.	DP=109;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,109,0:109:99:3980,0,3980:0,0,64,45
+gi|448814763|ref|NC_000962.3|	66285	.	C	G,<NON_REF>	2074	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2104,0,2104:0,0,20,33
+gi|448814763|ref|NC_000962.3|	69871	.	C	T,<NON_REF>	3532	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3562,0,3562:0,0,42,59
+gi|448814763|ref|NC_000962.3|	69989	.	G	A,<NON_REF>	1569	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,50,0:50:99:1599,0,1599:0,0,16,34
+gi|448814763|ref|NC_000962.3|	70816	.	A	G,<NON_REF>	3136	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3166,0,3166:0,0,59,24
+gi|448814763|ref|NC_000962.3|	71336	.	G	C,<NON_REF>	1177	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1207,0,1207:0,0,25,5
+gi|448814763|ref|NC_000962.3|	71584	.	C	CCGAGCGCTGTTCTGGCGCTAATCTGACGCTAGAATAG,<NON_REF>	3237.97	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.86;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:3277,0,3287:0,0,28,19
+gi|448814763|ref|NC_000962.3|	75264	.	C	T,<NON_REF>	2055	.	DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,58,0:58:99:2085,0,2085:0,0,24,34
+gi|448814763|ref|NC_000962.3|	75940	.	G	C,<NON_REF>	2042	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2072,0,2072:0,0,32,23
+gi|448814763|ref|NC_000962.3|	80616	.	C	G,<NON_REF>	3150	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:3180,0,3180:0,0,39,42
+gi|448814763|ref|NC_000962.3|	83982	.	A	G,<NON_REF>	3138	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,82,0:82:99:3168,0,3168:0,0,38,44
+gi|448814763|ref|NC_000962.3|	86576	.	G	A,<NON_REF>	2322	.	DP=65;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,65,0:65:99:2352,0,2352:0,0,31,34
+gi|448814763|ref|NC_000962.3|	92199	.	T	G,<NON_REF>	697	.	DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,20,0:20:99:727,0,727:0,0,15,5
+gi|448814763|ref|NC_000962.3|	95591	.	G	T,<NON_REF>	2735	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2765,0,2765:0,0,29,48
+gi|448814763|ref|NC_000962.3|	97388	.	G	T,<NON_REF>	3943	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3973,0,3973:0,0,57,56
+gi|448814763|ref|NC_000962.3|	103836	.	G	T,<NON_REF>	413	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.44;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:443,0,443:0,0,0,12
+gi|448814763|ref|NC_000962.3|	104712	.	C	T,<NON_REF>	518	.	DP=15;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.35;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,15,0:15:99:548,0,548:0,0,14,1
+gi|448814763|ref|NC_000962.3|	109812	.	C	T,<NON_REF>	109	.	BaseQRankSum=-4.970;ClippingRankSum=2.099;DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.061;ReadPosRankSum=0.191	GT:AD:DP:GQ:PL:SB	1:26,33,0:59:99:139,0,1182:13,13,19,14
+gi|448814763|ref|NC_000962.3|	116000	.	T	G,<NON_REF>	2435	.	DP=63;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,63,0:63:99:2465,0,2465:0,0,40,23
+gi|448814763|ref|NC_000962.3|	119669	.	G	A,<NON_REF>	3467	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3497,0,3497:0,0,48,48
+gi|448814763|ref|NC_000962.3|	122109	.	A	G,<NON_REF>	2888	.	DP=79;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,79,0:79:99:2918,0,2918:0,0,53,26
+gi|448814763|ref|NC_000962.3|	125830	.	G	GA,<NON_REF>	2470.97	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,76,0:76:99:2510,0,2510:0,0,20,56
+gi|448814763|ref|NC_000962.3|	128338	.	G	C,<NON_REF>	1736	.	DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,45,0:45:99:1766,0,1766:0,0,24,21
+gi|448814763|ref|NC_000962.3|	131174	.	T	TG,<NON_REF>	2379.97	.	DP=71;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,67,0:67:99:2419,0,2419:0,0,40,27
+gi|448814763|ref|NC_000962.3|	132417	.	C	G,<NON_REF>	490	.	DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,13,0:13:99:520,0,520:0,0,1,12
+gi|448814763|ref|NC_000962.3|	133839	.	C	T,<NON_REF>	2631	.	DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,75,0:75:99:2661,0,2661:0,0,35,40
+gi|448814763|ref|NC_000962.3|	137850	.	GT	G,<NON_REF>	2180.97	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,68,0:68:99:2220,0,2220:0,0,34,34
+gi|448814763|ref|NC_000962.3|	144390	.	G	A,<NON_REF>	1439	.	DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,41,0:41:99:1469,0,1469:0,0,28,13
+gi|448814763|ref|NC_000962.3|	146087	.	T	C,<NON_REF>	2308	.	DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,59,0:59:99:2338,0,2338:0,0,30,29
+gi|448814763|ref|NC_000962.3|	147985	.	C	T,<NON_REF>	2152	.	DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,62,0:62:99:2182,0,2182:0,0,24,38
+gi|448814763|ref|NC_000962.3|	150326	.	CAATCGGCCT	C,<NON_REF>	140.97	.	DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=59.60;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,4,0:4:99:180,0,180:0,0,2,2
+gi|448814763|ref|NC_000962.3|	151177	.	G	C,<NON_REF>	2127	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2157,0,2157:0,0,37,19
+gi|448814763|ref|NC_000962.3|	154283	.	T	C,<NON_REF>	2901	.	BaseQRankSum=1.646;ClippingRankSum=-0.909;DP=80;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.73;MQ0=0;MQRankSum=-1.213;ReadPosRankSum=1.342	GT:AD:DP:GQ:PL:SB	1:1,79,0:80:99:2931,0,2955:1,0,38,41
+gi|448814763|ref|NC_000962.3|	155293	.	G	A,<NON_REF>	1652	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1682,0,1682:0,0,27,22
+gi|448814763|ref|NC_000962.3|	163573	.	A	C,<NON_REF>	1809	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1839,0,1839:0,0,23,25
+gi|448814763|ref|NC_000962.3|	174684	.	C	A,<NON_REF>	1780	.	DP=52;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,52,0:52:99:1810,0,1810:0,0,30,22
+gi|448814763|ref|NC_000962.3|	177596	.	T	C,<NON_REF>	2967	.	DP=78;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,78,0:78:99:2997,0,2997:0,0,63,15
+gi|448814763|ref|NC_000962.3|	177857	.	G	A,<NON_REF>	1506	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,42,0:42:99:1536,0,1536:0,0,1,41
+gi|448814763|ref|NC_000962.3|	178946	.	C	T,<NON_REF>	1368	.	DP=40;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,40,0:40:99:1398,0,1398:0,0,12,28
+gi|448814763|ref|NC_000962.3|	187584	.	A	G,<NON_REF>	2307	.	DP=60;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2337,0,2337:0,0,29,31
+gi|448814763|ref|NC_000962.3|	187738	.	G	A,<NON_REF>	2535	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2565,0,2565:0,0,36,36
+gi|448814763|ref|NC_000962.3|	188800	.	T	C,<NON_REF>	1495	.	DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,41,0:41:99:1525,0,1525:0,0,20,21
+gi|448814763|ref|NC_000962.3|	191853	.	A	G,<NON_REF>	2101	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2131,0,2131:0,0,21,34
+gi|448814763|ref|NC_000962.3|	194681	.	G	C,<NON_REF>	1539	.	DP=39;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,39,0:39:99:1569,0,1569:0,0,13,26
+gi|448814763|ref|NC_000962.3|	196642	.	C	T,<NON_REF>	4724	.	DP=132;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,132,0:132:99:4754,0,4754:0,0,59,73
+gi|448814763|ref|NC_000962.3|	206339	.	T	C,<NON_REF>	2188	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2218,0,2218:0,0,33,24
+gi|448814763|ref|NC_000962.3|	220050	.	C	T,<NON_REF>	981	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1011,0,1011:0,0,3,25
+gi|448814763|ref|NC_000962.3|	223942	.	T	C,<NON_REF>	486	.	DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,13,0:13:99:516,0,516:0,0,10,3
+gi|448814763|ref|NC_000962.3|	225323	.	T	C,<NON_REF>	2159	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2189,0,2189:0,0,29,28
+gi|448814763|ref|NC_000962.3|	227098	.	T	C,<NON_REF>	2543	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2573,0,2573:0,0,31,35
+gi|448814763|ref|NC_000962.3|	231114	.	C	G,<NON_REF>	4042	.	DP=106;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,106,0:106:99:4072,0,4072:0,0,54,52
+gi|448814763|ref|NC_000962.3|	232574	.	G	T,<NON_REF>	2181	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,61,0:61:99:2211,0,2211:0,0,32,29
+gi|448814763|ref|NC_000962.3|	234477	.	T	G,<NON_REF>	329	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:359,0,359:0,0,8,4
+gi|448814763|ref|NC_000962.3|	234496	.	C	CGT,<NON_REF>	995.97	.	DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,20,0:20:99:1035,0,1035:0,0,12,8
+gi|448814763|ref|NC_000962.3|	251468	.	G	T,<NON_REF>	2046	.	DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,62,0:62:99:2076,0,2076:0,0,43,19
+gi|448814763|ref|NC_000962.3|	261869	.	T	C,<NON_REF>	394	.	DP=11;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,11,0:11:99:424,0,424:0,0,2,9
+gi|448814763|ref|NC_000962.3|	265475	.	G	A,<NON_REF>	4124	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,114,0:114:99:4154,0,4154:0,0,48,66
+gi|448814763|ref|NC_000962.3|	265554	.	A	C,<NON_REF>	4281	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:4311,0,4311:0,0,56,57
+gi|448814763|ref|NC_000962.3|	265968	.	C	G,<NON_REF>	2091	.	DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,54,0:54:99:2121,0,2121:0,0,22,32
+gi|448814763|ref|NC_000962.3|	278681	.	C	G,<NON_REF>	2284	.	DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,59,0:59:99:2314,0,2314:0,0,36,23
+gi|448814763|ref|NC_000962.3|	283614	.	T	C,<NON_REF>	1794	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:1824,0,1824:0,0,30,17
+gi|448814763|ref|NC_000962.3|	284623	.	G	A,<NON_REF>	1019	.	DP=31;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,31,0:31:99:1049,0,1049:0,0,22,9
+gi|448814763|ref|NC_000962.3|	285772	.	A	C,<NON_REF>	1085	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1115,0,1115:0,0,11,17
+gi|448814763|ref|NC_000962.3|	285871	.	A	G,<NON_REF>	1112	.	DP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,29,0:29:99:1142,0,1142:0,0,19,10
+gi|448814763|ref|NC_000962.3|	293628	.	A	AC,<NON_REF>	1458.97	.	DP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1498,0,1498:0,0,36,10
+gi|448814763|ref|NC_000962.3|	301290	.	G	A,<NON_REF>	2691	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:2721,0,2721:0,0,41,40
+gi|448814763|ref|NC_000962.3|	304679	.	G	T,<NON_REF>	3530	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3560,0,3560:0,0,46,55
+gi|448814763|ref|NC_000962.3|	304923	.	A	G,<NON_REF>	3082	.	DP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,84,0:84:99:3112,0,3112:0,0,52,32
+gi|448814763|ref|NC_000962.3|	310973	.	G	A,<NON_REF>	1535	.	DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,45,0:45:99:1565,0,1565:0,0,28,17
+gi|448814763|ref|NC_000962.3|	311613	.	G	T,<NON_REF>	2695	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2725,0,2725:0,0,44,33
+gi|448814763|ref|NC_000962.3|	315502	.	C	A,<NON_REF>	1010	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1040,0,1040:0,0,14,16
+gi|448814763|ref|NC_000962.3|	320038	.	G	A,<NON_REF>	626	.	DP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,19,0:19:99:656,0,656:0,0,9,10
+gi|448814763|ref|NC_000962.3|	328641	.	G	T,<NON_REF>	1816	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,51,0:51:99:1846,0,1846:0,0,17,34
+gi|448814763|ref|NC_000962.3|	335971	.	A	G,<NON_REF>	1022	.	DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=63.45;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,25,0:25:99:1052,0,1052:0,0,12,13
+gi|448814763|ref|NC_000962.3|	336047	.	C	G,<NON_REF>	1353	.	BaseQRankSum=-0.603;ClippingRankSum=-1.789;DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.67;MQ0=0;MQRankSum=1.492;ReadPosRankSum=-2.141	GT:AD:DP:GQ:PL:SB	1:14,43,0:57:99:1383,0,2013:7,7,18,25
+gi|448814763|ref|NC_000962.3|	336050	.	A	G,<NON_REF>	1240	.	BaseQRankSum=3.331;ClippingRankSum=-0.852;DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.28;MQ0=0;MQRankSum=-0.808;ReadPosRankSum=-1.826	GT:AD:DP:GQ:PL:SB	1:14,35,0:49:99:1270,0,1900:7,7,12,23
+gi|448814763|ref|NC_000962.3|	336053	.	G	C,<NON_REF>	870	.	BaseQRankSum=-0.454;ClippingRankSum=-0.570;DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.16;MQ0=0;MQRankSum=0.896;ReadPosRankSum=-1.780	GT:AD:DP:GQ:PL:SB	1:14,33,0:47:99:900,0,1530:7,7,11,22
+gi|448814763|ref|NC_000962.3|	336191	.	C	T,<NON_REF>	1569	.	DP=44;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.79;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,44,0:44:99:1599,0,1599:0,0,38,6
+gi|448814763|ref|NC_000962.3|	336772	.	C	T,<NON_REF>	364	.	DP=9;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,9,0:9:99:394,0,394:0,0,1,8
+gi|448814763|ref|NC_000962.3|	336773	.	A	G,<NON_REF>	364	.	DP=8;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,8,0:8:99:394,0,394:0,0,1,7
+gi|448814763|ref|NC_000962.3|	336780	.	G	A,<NON_REF>	285	.	DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,4,0:4:99:315,0,315:0,0,0,4
+gi|448814763|ref|NC_000962.3|	336781	.	T	C,<NON_REF>	150	.	DP=3;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,3,0:3:99:180,0,180:0,0,0,3
+gi|448814763|ref|NC_000962.3|	336782	.	G	C,<NON_REF>	150	.	DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,2,0:2:99:180,0,180:0,0,0,2
+gi|448814763|ref|NC_000962.3|	338020	.	A	C,<NON_REF>	45	.	DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,2,0:2:75:75,0,75:0,0,2,0
+gi|448814763|ref|NC_000962.3|	338100	.	T	C,<NON_REF>	216	.	DP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,6,0:6:99:246,0,246:0,0,6,0
diff -r 000000000000 -r bf8841b0a6b0 test-data/variants_output1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/variants_output1.vcf	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,208 @@
+##fileformat=VCFv4.1
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
+##FILTER=<ID=LowQual,Description="Low quality">
+##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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 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=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 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=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false 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 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null 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">
+##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)
+##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive)
+##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive)
+##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive)
+##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive)
+##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive)
+##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive)
+##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive)
+##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive)
+##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive)
+##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive)
+##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive)
+##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive)
+##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive)
+##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive)
+##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive)
+##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive)
+##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive)
+##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive)
+##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive)
+##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive)
+##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive)
+##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive)
+##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive)
+##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive)
+##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive)
+##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive)
+##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive)
+##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive)
+##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive)
+##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive)
+##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive)
+##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive)
+##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive)
+##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive)
+##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive)
+##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive)
+##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive)
+##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive)
+##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive)
+##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive)
+##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive)
+##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive)
+##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive)
+##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive)
+##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive)
+##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive)
+##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive)
+##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive)
+##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive)
+##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive)
+##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive)
+##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive)
+##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive)
+##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive)
+##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive)
+##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive)
+##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive)
+##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive)
+##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive)
+##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive)
+##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive)
+##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive)
+##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive)
+##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive)
+##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=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##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=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##contig=<ID=gi|448814763|ref|NC_000962.3|,length=4411532>
+##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	./R_2117_866#L5-_.R
+gi|448814763|ref|NC_000962.3|	1977	.	A	G,<NON_REF>	1986	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2016,0,2016:0,0,11,42
+gi|448814763|ref|NC_000962.3|	4013	.	T	C,<NON_REF>	2081	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2111,0,2111:0,0,29,24
+gi|448814763|ref|NC_000962.3|	7362	.	G	C,<NON_REF>	3369	.	BaseQRankSum=1.693;ClippingRankSum=1.693;DP=88;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=0.827;ReadPosRankSum=1.614	GT:AD:DP:GQ:PL:SB	1:1,87,0:88:99:3399,0,3408:0,1,40,47
+gi|448814763|ref|NC_000962.3|	7585	.	G	C,<NON_REF>	2294	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2324,0,2324:0,0,36,24
+gi|448814763|ref|NC_000962.3|	9304	.	G	A,<NON_REF>	2343	.	DP=69;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2373,0,2373:0,0,31,38
+gi|448814763|ref|NC_000962.3|	11311	.	A	C,<NON_REF>	3627	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3657,0,3657:0,0,31,65
+gi|448814763|ref|NC_000962.3|	11370	.	C	T,<NON_REF>	2699	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2729,0,2729:0,0,21,56
+gi|448814763|ref|NC_000962.3|	11879	.	A	G,<NON_REF>	2659	.	DP=70;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,69,0:69:99:2689,0,2689:0,0,36,33
+gi|448814763|ref|NC_000962.3|	14785	.	T	C,<NON_REF>	3506	.	DP=90;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,90,0:90:99:3536,0,3536:0,0,38,52
+gi|448814763|ref|NC_000962.3|	21795	.	G	A,<NON_REF>	784	.	DP=24;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:814,0,814:0,0,8,16
+gi|448814763|ref|NC_000962.3|	24698	.	GCCGCGTTGCTCGGGGTAA	G,<NON_REF>	1536.97	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.01;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1576,0,1576:0,0,25,11
+gi|448814763|ref|NC_000962.3|	26959	.	C	G,<NON_REF>	2474	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2504,0,2504:0,0,41,25
+gi|448814763|ref|NC_000962.3|	29482	.	CA	C,<NON_REF>	2528.97	.	DP=74;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.14;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2568,0,2568:0,0,34,38
+gi|448814763|ref|NC_000962.3|	30519	.	C	T,<NON_REF>	2289	.	BaseQRankSum=1.681;ClippingRankSum=0.026;DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.525;ReadPosRankSum=1.060	GT:AD:DP:GQ:PL:SB	1:1,66,0:67:99:2319,0,2329:1,0,47,19
+gi|448814763|ref|NC_000962.3|	30688	.	T	G,<NON_REF>	2109	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2139,0,2139:0,0,30,26
+gi|448814763|ref|NC_000962.3|	30943	.	C	T,<NON_REF>	1534	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1564,0,1564:0,0,28,21
+gi|448814763|ref|NC_000962.3|	31077	.	C	T,<NON_REF>	1499	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,43,0:43:99:1529,0,1529:0,0,24,19
+gi|448814763|ref|NC_000962.3|	32349	.	CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG	C,<NON_REF>	3070.97	.	DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=65.20;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,70,0:70:99:3110,0,3110:0,0,35,35
+gi|448814763|ref|NC_000962.3|	34044	.	T	C,<NON_REF>	3703	.	DP=94;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,94,0:94:99:3733,0,3733:0,0,60,34
+gi|448814763|ref|NC_000962.3|	37031	.	C	G,<NON_REF>	1773	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1803,0,1803:0,0,22,24
+gi|448814763|ref|NC_000962.3|	37910	.	C	A,<NON_REF>	3793	.	DP=113;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3823,0,3823:0,0,62,51
+gi|448814763|ref|NC_000962.3|	39223	.	GC	G,<NON_REF>	1460.97	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1500,0,1500:0,0,19,27
+gi|448814763|ref|NC_000962.3|	42967	.	G	C,<NON_REF>	2609	.	DP=67;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,67,0:67:99:2639,0,2639:0,0,15,52
+gi|448814763|ref|NC_000962.3|	50557	.	T	C,<NON_REF>	2896	.	DP=73;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,73,0:73:99:2926,0,2926:0,0,43,30
+gi|448814763|ref|NC_000962.3|	51949	.	A	G,<NON_REF>	3374	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,76,0:76:99:3404,0,3404:0,0,33,43
+gi|448814763|ref|NC_000962.3|	51954	.	T	A,<NON_REF>	3329	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,71,0:71:99:3359,0,3359:0,0,29,42
+gi|448814763|ref|NC_000962.3|	53785	.	C	G,<NON_REF>	3639	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3669,0,3669:0,0,54,42
+gi|448814763|ref|NC_000962.3|	54394	.	A	G,<NON_REF>	3218	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3248,0,3248:0,0,40,43
+gi|448814763|ref|NC_000962.3|	55553	.	C	CCGCCGT,<NON_REF>	942.97	.	DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=74.16;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,24,0:24:99:982,0,982:0,0,8,16
+gi|448814763|ref|NC_000962.3|	57393	.	A	T,<NON_REF>	1304	.	DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,36,0:36:99:1334,0,1334:0,0,32,4
+gi|448814763|ref|NC_000962.3|	62049	.	A	G,<NON_REF>	1820	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1850,0,1850:0,0,24,24
+gi|448814763|ref|NC_000962.3|	62657	.	G	A,<NON_REF>	3950	.	DP=109;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,109,0:109:99:3980,0,3980:0,0,64,45
+gi|448814763|ref|NC_000962.3|	66285	.	C	G,<NON_REF>	2074	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,53,0:53:99:2104,0,2104:0,0,20,33
+gi|448814763|ref|NC_000962.3|	69871	.	C	T,<NON_REF>	3532	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3562,0,3562:0,0,42,59
+gi|448814763|ref|NC_000962.3|	69989	.	G	A,<NON_REF>	1569	.	DP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,50,0:50:99:1599,0,1599:0,0,16,34
+gi|448814763|ref|NC_000962.3|	70816	.	A	G,<NON_REF>	3136	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,83,0:83:99:3166,0,3166:0,0,59,24
+gi|448814763|ref|NC_000962.3|	71336	.	G	C,<NON_REF>	1177	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1207,0,1207:0,0,25,5
+gi|448814763|ref|NC_000962.3|	71584	.	C	CCGAGCGCTGTTCTGGCGCTAATCTGACGCTAGAATAG,<NON_REF>	3237.97	.	DP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.86;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:3277,0,3287:0,0,28,19
+gi|448814763|ref|NC_000962.3|	75264	.	C	T,<NON_REF>	2055	.	DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,58,0:58:99:2085,0,2085:0,0,24,34
+gi|448814763|ref|NC_000962.3|	75940	.	G	C,<NON_REF>	2042	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2072,0,2072:0,0,32,23
+gi|448814763|ref|NC_000962.3|	80616	.	C	G,<NON_REF>	3150	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:3180,0,3180:0,0,39,42
+gi|448814763|ref|NC_000962.3|	83982	.	A	G,<NON_REF>	3138	.	DP=83;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,82,0:82:99:3168,0,3168:0,0,38,44
+gi|448814763|ref|NC_000962.3|	86576	.	G	A,<NON_REF>	2322	.	DP=65;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,65,0:65:99:2352,0,2352:0,0,31,34
+gi|448814763|ref|NC_000962.3|	92199	.	T	G,<NON_REF>	697	.	DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,20,0:20:99:727,0,727:0,0,15,5
+gi|448814763|ref|NC_000962.3|	95591	.	G	T,<NON_REF>	2735	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2765,0,2765:0,0,29,48
+gi|448814763|ref|NC_000962.3|	97388	.	G	T,<NON_REF>	3943	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:3973,0,3973:0,0,57,56
+gi|448814763|ref|NC_000962.3|	103836	.	G	T,<NON_REF>	413	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.44;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:443,0,443:0,0,0,12
+gi|448814763|ref|NC_000962.3|	104712	.	C	T,<NON_REF>	518	.	DP=15;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.35;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,15,0:15:99:548,0,548:0,0,14,1
+gi|448814763|ref|NC_000962.3|	109812	.	C	T,<NON_REF>	109	.	BaseQRankSum=-4.970;ClippingRankSum=2.099;DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.061;ReadPosRankSum=0.191	GT:AD:DP:GQ:PL:SB	1:26,33,0:59:99:139,0,1182:13,13,19,14
+gi|448814763|ref|NC_000962.3|	116000	.	T	G,<NON_REF>	2435	.	DP=63;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,63,0:63:99:2465,0,2465:0,0,40,23
+gi|448814763|ref|NC_000962.3|	119669	.	G	A,<NON_REF>	3467	.	DP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,96,0:96:99:3497,0,3497:0,0,48,48
+gi|448814763|ref|NC_000962.3|	122109	.	A	G,<NON_REF>	2888	.	DP=79;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,79,0:79:99:2918,0,2918:0,0,53,26
+gi|448814763|ref|NC_000962.3|	125830	.	G	GA,<NON_REF>	2470.97	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,76,0:76:99:2510,0,2510:0,0,20,56
+gi|448814763|ref|NC_000962.3|	128338	.	G	C,<NON_REF>	1736	.	DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,45,0:45:99:1766,0,1766:0,0,24,21
+gi|448814763|ref|NC_000962.3|	131174	.	T	TG,<NON_REF>	2379.97	.	DP=71;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,67,0:67:99:2419,0,2419:0,0,40,27
+gi|448814763|ref|NC_000962.3|	132417	.	C	G,<NON_REF>	490	.	DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,13,0:13:99:520,0,520:0,0,1,12
+gi|448814763|ref|NC_000962.3|	133839	.	C	T,<NON_REF>	2631	.	DP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,75,0:75:99:2661,0,2661:0,0,35,40
+gi|448814763|ref|NC_000962.3|	137850	.	GT	G,<NON_REF>	2180.97	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,68,0:68:99:2220,0,2220:0,0,34,34
+gi|448814763|ref|NC_000962.3|	144390	.	G	A,<NON_REF>	1439	.	DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,41,0:41:99:1469,0,1469:0,0,28,13
+gi|448814763|ref|NC_000962.3|	146087	.	T	C,<NON_REF>	2308	.	DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,59,0:59:99:2338,0,2338:0,0,30,29
+gi|448814763|ref|NC_000962.3|	147985	.	C	T,<NON_REF>	2152	.	DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,62,0:62:99:2182,0,2182:0,0,24,38
+gi|448814763|ref|NC_000962.3|	150326	.	CAATCGGCCT	C,<NON_REF>	140.97	.	DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=59.60;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,4,0:4:99:180,0,180:0,0,2,2
+gi|448814763|ref|NC_000962.3|	151177	.	G	C,<NON_REF>	2127	.	DP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,56,0:56:99:2157,0,2157:0,0,37,19
+gi|448814763|ref|NC_000962.3|	154283	.	T	C,<NON_REF>	2901	.	BaseQRankSum=1.646;ClippingRankSum=-0.909;DP=80;MLEAC=1,0;MLEAF=1.00,0.00;MQ=68.73;MQ0=0;MQRankSum=-1.213;ReadPosRankSum=1.342	GT:AD:DP:GQ:PL:SB	1:1,79,0:80:99:2931,0,2955:1,0,38,41
+gi|448814763|ref|NC_000962.3|	155293	.	G	A,<NON_REF>	1652	.	DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,49,0:49:99:1682,0,1682:0,0,27,22
+gi|448814763|ref|NC_000962.3|	163573	.	A	C,<NON_REF>	1809	.	DP=48;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,48,0:48:99:1839,0,1839:0,0,23,25
+gi|448814763|ref|NC_000962.3|	174684	.	C	A,<NON_REF>	1780	.	DP=52;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,52,0:52:99:1810,0,1810:0,0,30,22
+gi|448814763|ref|NC_000962.3|	177596	.	T	C,<NON_REF>	2967	.	DP=78;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,78,0:78:99:2997,0,2997:0,0,63,15
+gi|448814763|ref|NC_000962.3|	177857	.	G	A,<NON_REF>	1506	.	DP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,42,0:42:99:1536,0,1536:0,0,1,41
+gi|448814763|ref|NC_000962.3|	178946	.	C	T,<NON_REF>	1368	.	DP=40;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,40,0:40:99:1398,0,1398:0,0,12,28
+gi|448814763|ref|NC_000962.3|	187584	.	A	G,<NON_REF>	2307	.	DP=60;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,60,0:60:99:2337,0,2337:0,0,29,31
+gi|448814763|ref|NC_000962.3|	187738	.	G	A,<NON_REF>	2535	.	DP=72;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,72,0:72:99:2565,0,2565:0,0,36,36
+gi|448814763|ref|NC_000962.3|	188800	.	T	C,<NON_REF>	1495	.	DP=41;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,41,0:41:99:1525,0,1525:0,0,20,21
+gi|448814763|ref|NC_000962.3|	191853	.	A	G,<NON_REF>	2101	.	DP=55;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,55,0:55:99:2131,0,2131:0,0,21,34
+gi|448814763|ref|NC_000962.3|	194681	.	G	C,<NON_REF>	1539	.	DP=39;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,39,0:39:99:1569,0,1569:0,0,13,26
+gi|448814763|ref|NC_000962.3|	196642	.	C	T,<NON_REF>	4724	.	DP=132;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,132,0:132:99:4754,0,4754:0,0,59,73
+gi|448814763|ref|NC_000962.3|	206339	.	T	C,<NON_REF>	2188	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2218,0,2218:0,0,33,24
+gi|448814763|ref|NC_000962.3|	220050	.	C	T,<NON_REF>	981	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1011,0,1011:0,0,3,25
+gi|448814763|ref|NC_000962.3|	223942	.	T	C,<NON_REF>	486	.	DP=13;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,13,0:13:99:516,0,516:0,0,10,3
+gi|448814763|ref|NC_000962.3|	225323	.	T	C,<NON_REF>	2159	.	DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,57,0:57:99:2189,0,2189:0,0,29,28
+gi|448814763|ref|NC_000962.3|	227098	.	T	C,<NON_REF>	2543	.	DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,66,0:66:99:2573,0,2573:0,0,31,35
+gi|448814763|ref|NC_000962.3|	231114	.	C	G,<NON_REF>	4042	.	DP=106;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,106,0:106:99:4072,0,4072:0,0,54,52
+gi|448814763|ref|NC_000962.3|	232574	.	G	T,<NON_REF>	2181	.	DP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,61,0:61:99:2211,0,2211:0,0,32,29
+gi|448814763|ref|NC_000962.3|	234477	.	T	G,<NON_REF>	329	.	DP=12;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,12,0:12:99:359,0,359:0,0,8,4
+gi|448814763|ref|NC_000962.3|	234496	.	C	CGT,<NON_REF>	995.97	.	DP=20;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,20,0:20:99:1035,0,1035:0,0,12,8
+gi|448814763|ref|NC_000962.3|	251468	.	G	T,<NON_REF>	2046	.	DP=62;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,62,0:62:99:2076,0,2076:0,0,43,19
+gi|448814763|ref|NC_000962.3|	261869	.	T	C,<NON_REF>	394	.	DP=11;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,11,0:11:99:424,0,424:0,0,2,9
+gi|448814763|ref|NC_000962.3|	265475	.	G	A,<NON_REF>	4124	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,114,0:114:99:4154,0,4154:0,0,48,66
+gi|448814763|ref|NC_000962.3|	265554	.	A	C,<NON_REF>	4281	.	DP=114;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,113,0:113:99:4311,0,4311:0,0,56,57
+gi|448814763|ref|NC_000962.3|	265968	.	C	G,<NON_REF>	2091	.	DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,54,0:54:99:2121,0,2121:0,0,22,32
+gi|448814763|ref|NC_000962.3|	278681	.	C	G,<NON_REF>	2284	.	DP=59;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,59,0:59:99:2314,0,2314:0,0,36,23
+gi|448814763|ref|NC_000962.3|	283614	.	T	C,<NON_REF>	1794	.	DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,47,0:47:99:1824,0,1824:0,0,30,17
+gi|448814763|ref|NC_000962.3|	284623	.	G	A,<NON_REF>	1019	.	DP=31;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,31,0:31:99:1049,0,1049:0,0,22,9
+gi|448814763|ref|NC_000962.3|	285772	.	A	C,<NON_REF>	1085	.	DP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,28,0:28:99:1115,0,1115:0,0,11,17
+gi|448814763|ref|NC_000962.3|	285871	.	A	G,<NON_REF>	1112	.	DP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,29,0:29:99:1142,0,1142:0,0,19,10
+gi|448814763|ref|NC_000962.3|	293628	.	A	AC,<NON_REF>	1458.97	.	DP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,46,0:46:99:1498,0,1498:0,0,36,10
+gi|448814763|ref|NC_000962.3|	301290	.	G	A,<NON_REF>	2691	.	DP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,81,0:81:99:2721,0,2721:0,0,41,40
+gi|448814763|ref|NC_000962.3|	304679	.	G	T,<NON_REF>	3530	.	DP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,101,0:101:99:3560,0,3560:0,0,46,55
+gi|448814763|ref|NC_000962.3|	304923	.	A	G,<NON_REF>	3082	.	DP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,84,0:84:99:3112,0,3112:0,0,52,32
+gi|448814763|ref|NC_000962.3|	310973	.	G	A,<NON_REF>	1535	.	DP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,45,0:45:99:1565,0,1565:0,0,28,17
+gi|448814763|ref|NC_000962.3|	311613	.	G	T,<NON_REF>	2695	.	DP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,77,0:77:99:2725,0,2725:0,0,44,33
+gi|448814763|ref|NC_000962.3|	315502	.	C	A,<NON_REF>	1010	.	DP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,30,0:30:99:1040,0,1040:0,0,14,16
+gi|448814763|ref|NC_000962.3|	320038	.	G	A,<NON_REF>	626	.	DP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,19,0:19:99:656,0,656:0,0,9,10
+gi|448814763|ref|NC_000962.3|	328641	.	G	T,<NON_REF>	1816	.	DP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,51,0:51:99:1846,0,1846:0,0,17,34
+gi|448814763|ref|NC_000962.3|	335971	.	A	G,<NON_REF>	1022	.	DP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=63.45;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,25,0:25:99:1052,0,1052:0,0,12,13
+gi|448814763|ref|NC_000962.3|	336047	.	C	G,<NON_REF>	1353	.	BaseQRankSum=-0.603;ClippingRankSum=-1.789;DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.67;MQ0=0;MQRankSum=1.492;ReadPosRankSum=-2.141	GT:AD:DP:GQ:PL:SB	1:14,43,0:57:99:1383,0,2013:7,7,18,25
+gi|448814763|ref|NC_000962.3|	336050	.	A	G,<NON_REF>	1240	.	BaseQRankSum=3.331;ClippingRankSum=-0.852;DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.28;MQ0=0;MQRankSum=-0.808;ReadPosRankSum=-1.826	GT:AD:DP:GQ:PL:SB	1:14,35,0:49:99:1270,0,1900:7,7,12,23
+gi|448814763|ref|NC_000962.3|	336053	.	G	C,<NON_REF>	870	.	BaseQRankSum=-0.454;ClippingRankSum=-0.570;DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.16;MQ0=0;MQRankSum=0.896;ReadPosRankSum=-1.780	GT:AD:DP:GQ:PL:SB	1:14,33,0:47:99:900,0,1530:7,7,11,22
+gi|448814763|ref|NC_000962.3|	336191	.	C	T,<NON_REF>	1569	.	DP=44;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.79;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,44,0:44:99:1599,0,1599:0,0,38,6
+gi|448814763|ref|NC_000962.3|	336772	.	C	T,<NON_REF>	364	.	DP=9;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,9,0:9:99:394,0,394:0,0,1,8
+gi|448814763|ref|NC_000962.3|	336773	.	A	G,<NON_REF>	364	.	DP=8;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,8,0:8:99:394,0,394:0,0,1,7
+gi|448814763|ref|NC_000962.3|	336780	.	G	A,<NON_REF>	285	.	DP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,4,0:4:99:315,0,315:0,0,0,4
+gi|448814763|ref|NC_000962.3|	336781	.	T	C,<NON_REF>	150	.	DP=3;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,3,0:3:99:180,0,180:0,0,0,3
+gi|448814763|ref|NC_000962.3|	336782	.	G	C,<NON_REF>	150	.	DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,2,0:2:99:180,0,180:0,0,0,2
+gi|448814763|ref|NC_000962.3|	338020	.	A	C,<NON_REF>	45	.	DP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,2,0:2:75:75,0,75:0,0,2,0
+gi|448814763|ref|NC_000962.3|	338100	.	T	C,<NON_REF>	216	.	DP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0	GT:AD:DP:GQ:PL:SB	1:0,6,0:6:99:246,0,246:0,0,6,0