##fileformat=VCFv4.1
##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=MLPSAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample">
##FORMAT=<ID=MLPSAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=UnifiedGenotyper,Version=3.3-0-g37228af,Date="Wed Jun 10 08:15:53 CEST 2015",Epoch=1433916953839,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[SRR566635.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=NC_002695.1.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=true useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 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=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##contig=<ID=gi|15829254|ref|NC_002695.1|,length=5498450>
##reference=file:///home/fabio/Coding/Python/bioinformatics/data_analysis_project/costalab/data_analysis/cse_results/escherichia_coli/O157:H7 Sakai/IonTorrentPGM_mem/SRX185723/SRR566635/NC_002695.1.fasta
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	rgsm
gi|15829254|ref|NC_002695.1|	270484	.	G	C	2747	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.612;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=3.4380;MLEAC=1;MLEAF=1.00;MQ=59.89;MQ0=0;MQRankSum=1.521;QD=23.68;ReadPosRankSum=-1.009;SOR=0.268	GT:AD:DP:GQ:PL	1:1,115:116:99:2777,0
gi|15829254|ref|NC_002695.1|	270502	.	G	A	2924	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.948;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=2.6493;MLEAC=1;MLEAF=1.00;MQ=59.26;MQ0=0;MQRankSum=1.667;QD=27.58;ReadPosRankSum=1.667;SOR=0.281	GT:AD:DP:GQ:PL	1:1,105:106:99:2954,0
gi|15829254|ref|NC_002695.1|	270545	.	A	C	2121	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.084;DP=109;Dels=0.01;FS=5.100;HaplotypeScore=23.5544;MLEAC=1;MLEAF=1.00;MQ=49.74;MQ0=3;MQRankSum=-1.031;QD=19.46;ReadPosRankSum=-0.760;SOR=0.425	GT:AD:DP:GQ:PL	1:5,103:108:99:2151,0
gi|15829254|ref|NC_002695.1|	270562	.	G	C	2366	.	AC=1;AF=1.00;AN=1;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=5.2793;MLEAC=1;MLEAF=1.00;MQ=48.85;MQ0=3;QD=22.75;SOR=0.818	GT:AD:DP:GQ:PL	1:1,103:104:99:2396,0
gi|15829254|ref|NC_002695.1|	270577	.	G	A	559	.	AC=1;AF=1.00;AN=1;BaseQRankSum=4.123;DP=63;Dels=0.00;FS=67.351;HaplotypeScore=61.7544;MLEAC=1;MLEAF=1.00;MQ=41.28;MQ0=3;MQRankSum=4.843;QD=8.87;ReadPosRankSum=-2.054;SOR=7.167	GT:AD:DP:GQ:PL	1:28,35:63:99:589,0
gi|15829254|ref|NC_002695.1|	270584	.	G	A	1197	.	AC=1;AF=1.00;AN=1;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=32.4027;MLEAC=1;MLEAF=1.00;MQ=38.79;MQ0=3;QD=21.00;SOR=0.931	GT:AD:DP:GQ:PL	1:0,57:57:99:1227,0
gi|15829254|ref|NC_002695.1|	270596	.	T	G	327	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.330;DP=51;Dels=0.02;FS=0.000;HaplotypeScore=28.8469;MLEAC=1;MLEAF=1.00;MQ=35.57;MQ0=3;MQRankSum=-0.578;QD=6.41;ReadPosRankSum=1.238;SOR=0.613	GT:AD:DP:GQ:PL	1:1,48:50:99:357,0
gi|15829254|ref|NC_002695.1|	270598	.	C	G	809	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.513;DP=52;Dels=0.02;FS=0.000;HaplotypeScore=29.6561;MLEAC=1;MLEAF=1.00;MQ=36.19;MQ0=3;MQRankSum=-0.852;QD=15.56;ReadPosRankSum=0.256;SOR=0.303	GT:AD:DP:GQ:PL	1:3,48:51:99:839,0
gi|15829254|ref|NC_002695.1|	270627	.	A	G	2705	.	AC=1;AF=1.00;AN=1;DP=103;Dels=0.01;FS=0.000;HaplotypeScore=5.0818;MLEAC=1;MLEAF=1.00;MQ=50.91;MQ0=2;QD=26.26;SOR=0.957	GT:AD:DP:GQ:PL	1:0,102:102:99:2735,0
gi|15829254|ref|NC_002695.1|	270646	.	C	A	2337	.	AC=1;AF=1.00;AN=1;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=7.7758;MLEAC=1;MLEAF=1.00;MQ=56.60;MQ0=0;QD=28.85;SOR=1.416	GT:AD:DP:GQ:PL	1:0,81:81:99:2367,0
gi|15829254|ref|NC_002695.1|	270666	.	T	C	1618	.	AC=1;AF=1.00;AN=1;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=59.17;MQ0=0;QD=29.42;SOR=1.609	GT:AD:DP:GQ:PL	1:0,55:55:99:1648,0
gi|15829254|ref|NC_002695.1|	270668	.	C	G	1410	.	AC=1;AF=1.00;AN=1;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=59.15;MQ0=0;QD=26.11;SOR=1.567	GT:AD:DP:GQ:PL	1:0,54:54:99:1440,0
gi|15829254|ref|NC_002695.1|	270674	.	C	G	946	.	AC=1;AF=1.00;AN=1;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=58.81;MQ0=0;QD=16.89;SOR=1.609	GT:AD:DP:GQ:PL	1:0,56:56:99:976,0
gi|15829254|ref|NC_002695.1|	338461	.	A	T	673	.	AC=1;AF=1.00;AN=1;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.04;SOR=1.270	GT:AD:DP:GQ:PL	1:0,24:24:99:703,0
gi|15829254|ref|NC_002695.1|	375317	.	A	C	3402	.	AC=1;AF=1.00;AN=1;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=7.2336;MLEAC=1;MLEAF=1.00;MQ=59.76;MQ0=1;QD=27.44;SOR=0.709	GT:AD:DP:GQ:PL	1:0,124:124:99:3432,0
gi|15829254|ref|NC_002695.1|	415750	.	G	T	1524	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.682;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=5.2777;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.481;QD=22.09;ReadPosRankSum=-0.176;SOR=0.302	GT:AD:DP:GQ:PL	1:1,68:69:99:1554,0
gi|15829254|ref|NC_002695.1|	431214	.	C	G	2393	.	AC=1;AF=1.00;AN=1;DP=89;Dels=0.01;FS=0.000;HaplotypeScore=6.3675;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.89;SOR=0.716	GT:AD:DP:GQ:PL	1:0,87:88:99:2423,0
gi|15829254|ref|NC_002695.1|	474603	.	C	A	492	.	AC=1;AF=1.00;AN=1;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=1.00;MQ=59.92;MQ0=0;QD=20.50;SOR=1.270	GT:AD:DP:GQ:PL	1:0,24:24:99:522,0
gi|15829254|ref|NC_002695.1|	517475	.	C	A	444	.	AC=1;AF=1.00;AN=1;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.37;SOR=0.693	GT:AD:DP:GQ:PL	1:0,18:19:99:474,0
gi|15829254|ref|NC_002695.1|	616890	.	C	T	97	.	AC=1;AF=1.00;AN=1;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=59.80;MQ0=0;QD=19.40;SOR=1.022	GT:AD:DP:GQ:PL	1:0,5:5:99:127,0
gi|15829254|ref|NC_002695.1|	730801	.	A	C	1264	.	AC=1;AF=1.00;AN=1;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.9399;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.89;SOR=1.132	GT:AD:DP:GQ:PL	1:0,47:47:99:1294,0
gi|15829254|ref|NC_002695.1|	745039	.	A	T	765	.	AC=1;AF=1.00;AN=1;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.42;SOR=1.022	GT:AD:DP:GQ:PL	1:0,26:26:99:795,0
gi|15829254|ref|NC_002695.1|	812703	.	T	C	59	.	AC=1;AF=1.00;AN=1;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.75;SOR=0.693	GT:AD:DP:GQ:PL	1:0,4:4:89:89,0
gi|15829254|ref|NC_002695.1|	935573	.	A	C	101	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.736;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.6155;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=14.43;ReadPosRankSum=-0.736;SOR=0.707	GT:AD:DP:GQ:PL	1:1,5:7:99:131,0
gi|15829254|ref|NC_002695.1|	1256941	.	C	T	1233	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.361;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=8.6575;MLEAC=1;MLEAF=1.00;MQ=57.45;MQ0=0;MQRankSum=1.588;QD=25.69;ReadPosRankSum=1.372;SOR=0.422	GT:AD:DP:GQ:PL	1:1,47:48:99:1263,0
gi|15829254|ref|NC_002695.1|	1385085	.	A	G	1110	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.828;DP=95;Dels=0.00;FS=1.806;HaplotypeScore=3.4830;MLEAC=1;MLEAF=1.00;MQ=59.70;MQ0=0;MQRankSum=1.030;QD=11.68;ReadPosRankSum=1.265;SOR=0.507	GT:AD:DP:GQ:PL	1:29,66:95:99:1140,0
gi|15829254|ref|NC_002695.1|	1385453	.	G	T	247	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.338;DP=38;Dels=0.00;FS=1.342;HaplotypeScore=3.2783;MLEAC=1;MLEAF=1.00;MQ=55.22;MQ0=0;MQRankSum=-2.062;QD=6.50;ReadPosRankSum=-1.231;SOR=0.845	GT:AD:DP:GQ:PL	1:13,25:38:99:277,0
gi|15829254|ref|NC_002695.1|	1385455	.	G	A	239	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.400;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=4.0669;MLEAC=1;MLEAF=1.00;MQ=55.22;MQ0=0;MQRankSum=-1.662;QD=6.29;ReadPosRankSum=-1.200;SOR=0.845	GT:AD:DP:GQ:PL	1:13,25:38:99:269,0
gi|15829254|ref|NC_002695.1|	1385465	.	G	A	356	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.472;DP=35;Dels=0.00;FS=3.401;HaplotypeScore=1.6553;MLEAC=1;MLEAF=1.00;MQ=54.04;MQ0=0;MQRankSum=-3.080;QD=10.17;ReadPosRankSum=-1.682;SOR=0.863	GT:AD:DP:GQ:PL	1:11,24:35:99:386,0
gi|15829254|ref|NC_002695.1|	1385616	.	T	C	76	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.087;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=1.00;MQ=54.54;MQ0=0;MQRankSum=-1.268;QD=4.22;ReadPosRankSum=-0.815;SOR=0.627	GT:AD:DP:GQ:PL	1:7,11:18:99:106,0
gi|15829254|ref|NC_002695.1|	1404441	.	G	A	98	.	AC=1;AF=1.00;AN=1;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=1;MLEAF=1.00;MQ=56.71;MQ0=0;QD=19.60;SOR=1.022	GT:AD:DP:GQ:PL	1:0,5:5:99:128,0
gi|15829254|ref|NC_002695.1|	1432771	.	T	C	235	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.315;DP=59;Dels=0.00;FS=1.757;HaplotypeScore=0.9332;MLEAC=1;MLEAF=1.00;MQ=15.85;MQ0=4;MQRankSum=0.755;QD=3.98;ReadPosRankSum=2.673;SOR=0.339	GT:AD:DP:GQ:PL	1:24,35:59:99:265,0
gi|15829254|ref|NC_002695.1|	1681338	.	C	G	1097	.	AC=1;AF=1.00;AN=1;BaseQRankSum=3.040;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=1.9700;MLEAC=1;MLEAF=1.00;MQ=59.85;MQ0=0;MQRankSum=-0.429;QD=21.51;ReadPosRankSum=-1.623;SOR=1.509	GT:AD:DP:GQ:PL	1:4,47:51:99:1127,0
gi|15829254|ref|NC_002695.1|	1681339	.	G	C	973	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.734;DP=51;Dels=0.00;FS=4.649;HaplotypeScore=1.9700;MLEAC=1;MLEAF=1.00;MQ=59.85;MQ0=0;MQRankSum=-0.018;QD=19.08;ReadPosRankSum=-1.591;SOR=1.108	GT:AD:DP:GQ:PL	1:4,46:51:99:1003,0
gi|15829254|ref|NC_002695.1|	1784838	.	A	G	1045	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.299;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=5.4844;MLEAC=1;MLEAF=1.00;MQ=57.80;MQ0=0;MQRankSum=1.547;QD=18.33;ReadPosRankSum=1.670;SOR=0.269	GT:AD:DP:GQ:PL	1:1,56:57:99:1075,0
gi|15829254|ref|NC_002695.1|	2049909	.	T	G	445	.	AC=1;AF=1.00;AN=1;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=59.18;MQ0=0;QD=26.18;SOR=0.804	GT:AD:DP:GQ:PL	1:0,17:17:99:475,0
gi|15829254|ref|NC_002695.1|	2049911	.	C	G	461	.	AC=1;AF=1.00;AN=1;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=59.18;MQ0=0;QD=27.12;SOR=0.804	GT:AD:DP:GQ:PL	1:0,17:17:99:491,0
gi|15829254|ref|NC_002695.1|	2049912	.	T	A	447	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.964;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=59.22;MQ0=0;MQRankSum=-1.349;QD=24.83;ReadPosRankSum=1.349;SOR=0.395	GT:AD:DP:GQ:PL	1:1,17:18:99:477,0
gi|15829254|ref|NC_002695.1|	2283012	.	T	G	218	.	AC=1;AF=1.00;AN=1;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=1;MLEAF=1.00;MQ=60.77;MQ0=0;QD=15.57;SOR=0.976	GT:AD:DP:GQ:PL	1:0,14:14:99:248,0
gi|15829254|ref|NC_002695.1|	3317204	.	T	C	120	.	AC=1;AF=1.00;AN=1;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.00;SOR=1.022	GT:AD:DP:GQ:PL	1:0,5:5:99:150,0
gi|15829254|ref|NC_002695.1|	3637135	.	T	C	1371	.	AC=1;AF=1.00;AN=1;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=4.6134;MLEAC=1;MLEAF=1.00;MQ=59.81;MQ0=0;QD=25.39;SOR=0.767	GT:AD:DP:GQ:PL	1:0,54:54:99:1401,0
gi|15829254|ref|NC_002695.1|	3817025	.	G	A	1227	.	AC=1;AF=1.00;AN=1;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.7005;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.27;SOR=0.829	GT:AD:DP:GQ:PL	1:0,45:45:99:1257,0
gi|15829254|ref|NC_002695.1|	3870643	.	C	A	368	.	AC=1;AF=1.00;AN=1;DP=33;Dels=0.03;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=27.60;MQ0=16;QD=11.15;SOR=0.941	GT:AD:DP:GQ:PL	1:15,17:32:99:398,0
gi|15829254|ref|NC_002695.1|	3957788	.	T	G	1583	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.155;DP=54;Dels=0.00;FS=3.174;HaplotypeScore=3.7780;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=1.540;QD=29.31;ReadPosRankSum=1.668;SOR=0.402	GT:AD:DP:GQ:PL	1:1,53:54:99:1613,0
gi|15829254|ref|NC_002695.1|	4100596	.	A	G	1730	.	AC=1;AF=1.00;AN=1;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=4.1563;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.70;SOR=0.836	GT:AD:DP:GQ:PL	1:0,73:73:99:1760,0
gi|15829254|ref|NC_002695.1|	4172246	.	G	T	2358	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.101;DP=85;Dels=0.00;FS=3.010;HaplotypeScore=1.9452;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=1.000;QD=27.74;ReadPosRankSum=2.015;SOR=0.144	GT:AD:DP:GQ:PL	1:2,83:85:99:2388,0
gi|15829254|ref|NC_002695.1|	4213984	.	G	T	934	.	AC=1;AF=1.00;AN=1;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=1;MLEAF=1.00;MQ=59.16;MQ0=1;QD=25.94;SOR=0.749	GT:AD:DP:GQ:PL	1:0,36:36:99:964,0
gi|15829254|ref|NC_002695.1|	4253956	.	G	T	2862	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.696;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=3.7202;MLEAC=1;MLEAF=1.00;MQ=59.69;MQ0=1;MQRankSum=-0.857;QD=29.81;ReadPosRankSum=1.331;SOR=0.259	GT:AD:DP:GQ:PL	1:1,95:96:99:2892,0
gi|15829254|ref|NC_002695.1|	4333553	.	T	A	511	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.909;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=1.00;MQ=59.16;MQ0=0;MQRankSum=1.909;QD=22.22;ReadPosRankSum=0.818;SOR=1.230	GT:AD:DP:GQ:PL	1:2,21:23:99:541,0
gi|15829254|ref|NC_002695.1|	4450419	.	C	T	481	.	AC=1;AF=1.00;AN=1;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.90;SOR=1.828	GT:AD:DP:GQ:PL	1:0,21:21:99:511,0
gi|15829254|ref|NC_002695.1|	4451098	.	G	A	953	.	AC=1;AF=1.00;AN=1;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.24;SOR=1.347	GT:AD:DP:GQ:PL	1:0,41:41:99:983,0
gi|15829254|ref|NC_002695.1|	4617900	.	C	A	60	.	AC=1;AF=1.00;AN=1;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.00;SOR=0.693	GT:AD:DP:GQ:PL	1:0,4:4:90:90,0
gi|15829254|ref|NC_002695.1|	4619636	.	C	T	1079	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.664;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=2.5606;MLEAC=1;MLEAF=1.00;MQ=59.43;MQ0=0;MQRankSum=1.529;QD=21.16;ReadPosRankSum=-0.374;SOR=0.746	GT:AD:DP:GQ:PL	1:1,50:51:99:1109,0
gi|15829254|ref|NC_002695.1|	4652077	.	T	A	735	.	AC=1;AF=1.00;AN=1;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=5.5326;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.27;SOR=0.693	GT:AD:DP:GQ:PL	1:0,33:33:99:765,0
gi|15829254|ref|NC_002695.1|	4652078	.	T	A	734	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.103;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=6.4991;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.788;QD=22.24;ReadPosRankSum=1.208;SOR=0.223	GT:AD:DP:GQ:PL	1:1,32:33:99:764,0
gi|15829254|ref|NC_002695.1|	4714723	.	C	A	993	.	AC=1;AF=1.00;AN=1;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.58;SOR=1.209	GT:AD:DP:GQ:PL	1:0,36:36:99:1023,0
gi|15829254|ref|NC_002695.1|	4933772	.	A	G	91	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.862;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=5.7202;MLEAC=1;MLEAF=1.00;MQ=58.87;MQ0=0;MQRankSum=-0.353;QD=1.05;ReadPosRankSum=-0.786;SOR=0.737	GT:AD:DP:GQ:PL	1:42,45:87:99:121,0
gi|15829254|ref|NC_002695.1|	4933785	.	A	T	363	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.376;DP=88;Dels=0.00;FS=0.790;HaplotypeScore=6.4232;MLEAC=1;MLEAF=1.00;MQ=59.13;MQ0=0;MQRankSum=-0.042;QD=4.13;ReadPosRankSum=1.021;SOR=0.599	GT:AD:DP:GQ:PL	1:41,47:88:99:393,0
gi|15829254|ref|NC_002695.1|	4933794	.	G	A	288	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.549;DP=76;Dels=0.00;FS=0.886;HaplotypeScore=3.4125;MLEAC=1;MLEAF=1.00;MQ=58.77;MQ0=1;MQRankSum=-0.154;QD=3.79;ReadPosRankSum=0.495;SOR=0.516	GT:AD:DP:GQ:PL	1:35,41:76:99:318,0
gi|15829254|ref|NC_002695.1|	4933833	.	T	C	194	.	AC=1;AF=1.00;AN=1;BaseQRankSum=3.245;DP=55;Dels=0.00;FS=1.037;HaplotypeScore=3.4553;MLEAC=1;MLEAF=1.00;MQ=59.30;MQ0=0;MQRankSum=-0.008;QD=3.53;ReadPosRankSum=-0.969;SOR=0.941	GT:AD:DP:GQ:PL	1:29,26:55:99:224,0
gi|15829254|ref|NC_002695.1|	4933892	.	A	C	436	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.239;DP=96;Dels=0.00;FS=5.686;HaplotypeScore=6.2289;MLEAC=1;MLEAF=1.00;MQ=59.00;MQ0=0;MQRankSum=-0.932;QD=4.54;ReadPosRankSum=-0.306;SOR=1.008	GT:AD:DP:GQ:PL	1:39,57:96:99:466,0
gi|15829254|ref|NC_002695.1|	4933905	.	T	C	351	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.054;DP=89;Dels=0.00;FS=5.877;HaplotypeScore=6.4151;MLEAC=1;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=-0.045;QD=3.94;ReadPosRankSum=-1.104;SOR=0.738	GT:AD:DP:GQ:PL	1:39,50:89:99:381,0
gi|15829254|ref|NC_002695.1|	4933908	.	G	A	248	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.610;DP=87;Dels=0.00;FS=8.744;HaplotypeScore=6.4151;MLEAC=1;MLEAF=1.00;MQ=58.99;MQ0=0;MQRankSum=-0.602;QD=2.85;ReadPosRankSum=-1.003;SOR=0.879	GT:AD:DP:GQ:PL	1:39,48:87:99:278,0
gi|15829254|ref|NC_002695.1|	4933914	.	T	A	275	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.167;DP=89;Dels=0.00;FS=5.478;HaplotypeScore=5.4486;MLEAC=1;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=-0.524;QD=3.09;ReadPosRankSum=-0.623;SOR=0.833	GT:AD:DP:GQ:PL	1:40,49:89:99:305,0
gi|15829254|ref|NC_002695.1|	4955567	.	T	C	51	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.969;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=40.75;MQ0=0;MQRankSum=-3.905;QD=2.22;ReadPosRankSum=-1.775;SOR=0.646	GT:AD:DP:GQ:PL	1:8,15:23:81:81,0
gi|15829254|ref|NC_002695.1|	4955594	.	C	A	187	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.209;DP=25;Dels=0.00;FS=1.833;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=38.35;MQ0=0;MQRankSum=-3.843;QD=7.48;ReadPosRankSum=-2.149;SOR=0.223	GT:AD:DP:GQ:PL	1:7,18:25:99:217,0
gi|15829254|ref|NC_002695.1|	4955597	.	A	C	137	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-0.878;DP=25;Dels=0.00;FS=1.922;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=38.35;MQ0=0;MQRankSum=-3.843;QD=5.48;ReadPosRankSum=-2.391;SOR=0.223	GT:AD:DP:GQ:PL	1:7,18:25:99:167,0
gi|15829254|ref|NC_002695.1|	4955600	.	G	A	124	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.340;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=-4.192;QD=4.59;ReadPosRankSum=-1.260;SOR=0.283	GT:AD:DP:GQ:PL	1:9,18:27:99:154,0
gi|15829254|ref|NC_002695.1|	4955609	.	A	G	94	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-1.003;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=-4.192;QD=3.48;ReadPosRankSum=-0.489;SOR=0.283	GT:AD:DP:GQ:PL	1:9,18:27:99:124,0
gi|15829254|ref|NC_002695.1|	4955612	.	A	G	113	.	AC=1;AF=1.00;AN=1;BaseQRankSum=-2.186;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9983;MLEAC=1;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=-4.192;QD=4.19;ReadPosRankSum=-0.540;SOR=0.283	GT:AD:DP:GQ:PL	1:9,18:27:99:143,0
gi|15829254|ref|NC_002695.1|	4955620	.	C	A	96	.	AC=1;AF=1.00;AN=1;BaseQRankSum=0.377;DP=27;Dels=0.00;FS=1.603;HaplotypeScore=1.9648;MLEAC=1;MLEAF=1.00;MQ=41.87;MQ0=0;MQRankSum=-4.293;QD=3.56;ReadPosRankSum=0.377;SOR=0.269	GT:AD:DP:GQ:PL	1:10,17:27:99:126,0
gi|15829254|ref|NC_002695.1|	4956017	.	C	A	49	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.688;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=1.00;MQ=59.32;MQ0=0;MQRankSum=-0.586;QD=1.40;ReadPosRankSum=-0.896;SOR=1.218	GT:AD:DP:GQ:PL	1:18,17:35:79:79,0
gi|15829254|ref|NC_002695.1|	4956176	.	G	T	271	.	AC=1;AF=1.00;AN=1;BaseQRankSum=1.754;DP=66;Dels=0.00;FS=0.940;HaplotypeScore=16.1247;MLEAC=1;MLEAF=1.00;MQ=58.14;MQ0=0;MQRankSum=-0.852;QD=4.11;ReadPosRankSum=-0.880;SOR=0.576	GT:AD:DP:GQ:PL	1:34,32:66:99:301,0
gi|15829254|ref|NC_002695.1|	4956194	.	T	C	574	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.907;DP=75;Dels=0.00;FS=0.890;HaplotypeScore=1.9330;MLEAC=1;MLEAF=1.00;MQ=57.60;MQ0=1;MQRankSum=-0.999;QD=7.65;ReadPosRankSum=-2.026;SOR=0.735	GT:AD:DP:GQ:PL	1:33,42:75:99:604,0
gi|15829254|ref|NC_002695.1|	4956236	.	C	A	42	.	AC=1;AF=1.00;AN=1;BaseQRankSum=3.367;DP=56;Dels=0.00;FS=2.363;HaplotypeScore=5.5832;MLEAC=1;MLEAF=1.00;MQ=57.60;MQ0=1;MQRankSum=-1.549;QD=0.75;ReadPosRankSum=1.255;SOR=0.369	GT:AD:DP:GQ:PL	1:29,27:56:72:72,0
gi|15829254|ref|NC_002695.1|	4956239	.	G	A	206	.	AC=1;AF=1.00;AN=1;BaseQRankSum=3.263;DP=56;Dels=0.00;FS=1.059;HaplotypeScore=4.6000;MLEAC=1;MLEAF=1.00;MQ=57.60;MQ0=1;MQRankSum=-2.086;QD=3.68;ReadPosRankSum=1.082;SOR=0.465	GT:AD:DP:GQ:PL	1:29,27:56:99:236,0
gi|15829254|ref|NC_002695.1|	5070594	.	G	C	158	.	AC=1;AF=1.00;AN=1;BaseQRankSum=2.520;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-0.896;QD=14.36;ReadPosRankSum=0.678;SOR=0.595	GT:AD:DP:GQ:PL	1:4,7:11:99:188,0
gi|15829254|ref|NC_002695.1|	5070601	.	C	A	393	.	AC=1;AF=1.00;AN=1;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.20;SOR=0.818	GT:AD:DP:GQ:PL	1:0,15:15:99:423,0
gi|15829254|ref|NC_002695.1|	5070620	.	C	T	463	.	AC=1;AF=1.00;AN=1;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.24;SOR=0.941	GT:AD:DP:GQ:PL	1:0,16:17:99:493,0
gi|15829254|ref|NC_002695.1|	5344115	.	G	C	1056	.	AC=1;AF=1.00;AN=1;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.7297;MLEAC=1;MLEAF=1.00;MQ=58.55;MQ0=0;QD=27.79;SOR=0.746	GT:AD:DP:GQ:PL	1:0,37:38:99:1086,0