##fileformat=VCFv4.0
##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="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=.,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=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##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=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
##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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/work/galaxy/database/files/013/dataset_13703.dat.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=tmpdir19945/reference.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=tmpdir19945/empty.rod downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=ALLOW_UNINDEXED_BAM num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=10.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 insertionStartProbability=0.0010 insertionEndProbability=0.5 alphaDeletionProbability=0.0010 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=40.0 indelHaplotypeSize=80 doContextDependentGapPenalties=false indelDebug=false s1=null s2=null dovit=false newlike=false exactCalculation=LINEAR_EXPERIMENTAL output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub verbose_mode=null metrics_file=null annotation=[]"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	RC1	RC10	RC2	RC3	RC4	RC5	RC6	RC7	RC8	RC9
LOC_Os01g44110.1	231	.	C	A	277.71	PASS	AC=8;AF=1.00;AN=8;DP=25;Dels=0.00;HRun=0;HaplotypeScore=0.2290;MQ=58.83;MQ0=0;QD=21.36;SB=-110.98;sumGLbyD=24.53	GT:AD:DP:GQ:PL	./.	1/1:0,4:4:12.02:120,12,0	./.	./.	1/1:0,2:1:2.99:24,3,0	1/1:0,2:2:6:54,6,0	1/1:0,5:4:12:117,12,0	./.	./.	./.
LOC_Os01g44110.1	471	.	G	A	2451.76	PASS	AC=20;AF=1.000;AN=20;DP=210;DS;Dels=0.00;HRun=2;HaplotypeScore=1.1160;MQ=58.60;MQ0=0;QD=11.68;SB=-1263.97;sumGLbyD=11.89	GT:AD:DP:GQ:PL	1/1:0,22:2:5.97:45,6,0	1/1:0,30:16:44.97:409,45,0	1/1:0,17:2:5.98:47,6,0	1/1:0,16:7:20.96:171,21,0	1/1:0,12:5:14.97:121,15,0	1/1:0,42:27:68.99:660,69,0	1/1:0,22:12:30:290,30,0	1/1:0,10:2:5.96:43,6,0	1/1:0,25:21:45.04:496,45,0	1/1:0,14:9:26.91:212,27,0
LOC_Os01g44110.1	512	.	T	C	549.45	PASS	AC=3;AF=0.167;AN=18;DP=165;DS;Dels=0.00;HRun=0;HaplotypeScore=0.5952;MQ=58.81;MQ0=0;QD=16.16;SB=-294.47;sumGLbyD=18.08	GT:AD:DP:GQ:PL	0/0:18,0:10:23.97:0,24,229	0/0:36,0:31:63.10:0,63,747	./.	0/0:12,0:7:21:0,21,190	0/0:5,0:1:2.99:0,3,24	1/1:0,26:22:57.05:564,57,0	0/0:14,0:10:24:0,24,259	0/1:0,7:2:0.98:50,6,0	0/0:22,0:20:36.09:0,36,472	0/0:12,0:8:15.02:0,15,181
LOC_Os01g62920.1	144	.	A	C	114.08	PASS	AC=6;AF=1.00;AN=6;DP=14;DS;Dels=0.00;HRun=1;HaplotypeScore=0.2980;MQ=58.66;MQ0=0;QD=12.68;SB=-49.95;sumGLbyD=17.09	GT:AD:DP:GQ:PL	./.	1/1:0,5:3:9:81,9,0	./.	1/1:0,2:2:3.01:44,3,0	./.	./.	./.	./.	1/1:0,2:1:3:25,3,0	./.
LOC_Os01g62920.1	145	.	C	A	10.49	LowQual	AC=1;AF=0.25;AN=4;DP=14;DS;Dels=0.00;HRun=3;HaplotypeScore=0.4470;MQ=58.66;MQ0=0;QD=5.25;SB=-23.24;sumGLbyD=23.05	GT:AD:DP:GQ:PL	./.	0/0:5,0:3:9.01:0,9,90	./.	0/1:0,2:2:1.76:44,3,0	./.	./.	./.	./.	./.	./.
LOC_Os01g62920.1	866	.	G	A	269.68	PASS	AC=14;AF=1.000;AN=14;DP=68;DS;Dels=0.00;HRun=1;HaplotypeScore=0.4022;MQ=47.27;MQ0=0;QD=4.82;SB=-111.70;sumGLbyD=5.68	GT:AD:DP:GQ:PL	./.	1/1:0,3:1:3:28,3,0	1/1:0,9:1:2.98:22,3,0	./.	1/1:0,6:3:8.99:75,9,0	1/1:0,10:1:2.99:24,3,0	1/1:0,11:3:8.96:69,9,0	1/1:1,9:1:2.99:24,3,0	1/1:0,7:3:6.01:68,6,0	./.
LOC_Os01g62920.1	867	.	A	C	540.82	PASS	AC=18;AF=1.000;AN=18;DP=68;DS;Dels=0.00;HRun=1;HaplotypeScore=0.4171;MQ=47.27;MQ0=0;QD=8.07;SB=-267.28;sumGLbyD=8.82	GT:AD:DP:GQ:PL	./.	1/1:0,3:1:2.99:24,3,0	1/1:0,9:1:2.98:22,3,0	1/1:0,5:1:2.99:23,3,0	1/1:0,6:3:8.98:73,9,0	1/1:0,10:4:12:105,12,0	1/1:0,11:5:14.96:120,15,0	1/1:0,10:1:2.98:22,3,0	1/1:0,7:6:12.02:141,12,0	1/1:0,6:2:5.99:53,6,0
LOC_Os01g62920.1	1602	.	T	C	866.26	PASS	AC=20;AF=1.000;AN=20;DP=102;DS;Dels=0.00;HRun=0;HaplotypeScore=0.3579;MQ=58.53;MQ0=0;QD=8.49;SB=-420.92;sumGLbyD=8.96	GT:AD:DP:GQ:PL	1/1:0,13:3:8.95:66,9,0	1/1:0,13:7:21:190,21,0	1/1:0,17:3:8.97:72,9,0	1/1:0,15:6:17.95:142,18,0	1/1:0,4:2:5.97:45,6,0	1/1:0,8:3:9:81,9,0	1/1:0,5:3:8.99:74,9,0	1/1:0,9:1:3.01:30,3,0	1/1:0,9:5:11.99:115,12,0	1/1:0,9:4:11.95:94,12,0
LOC_Os01g62920.1	1703	.	G	A	783.74	PASS	AC=5;AF=0.250;AN=20;DP=303;DS;Dels=0.00;HRun=2;HaplotypeScore=1.2246;MQ=58.50;MQ0=0;QD=8.52;SB=-411.95;sumGLbyD=9.37	GT:AD:DP:GQ:PL	0/0:24,0:11:29.94:0,30,260	0/0:50,0:31:81:0,81,798	0/0:18,0:8:23.93:0,24,190	0/0:29,0:13:38.93:0,39,323	0/0:20,0:9:23.96:0,24,217	1/1:0,42:24:62.98:588,63,0	0/0:24,0:15:36.02:0,36,372	1/1:0,20:5:14.94:116,15,0	0/0:45,0:33:66.08:0,66,766	0/1:8,22:8:2.02:156,2,0
LOC_Os01g62920.1	1721	.	A	G	2545.85	PASS	AC=18;AF=1.000;AN=18;DP=297;DS;Dels=0.00;HRun=0;HaplotypeScore=1.3126;MQ=58.68;MQ0=0;QD=9.06;SB=-1088.96;sumGLbyD=9.22	GT:AD:DP:GQ:PL	1/1:0,29:6:17.94:141,18,0	1/1:0,46:20:50.98:494,51,0	1/1:0,18:2:5.99:52,6,0	1/1:0,31:11:32.87:254,33,0	1/1:0,18:3:6.01:72,6,0	1/1:0,39:21:56.92:516,57,0	1/1:0,24:12:32.95:294,33,0	./.	1/1:0,43:24:54.01:570,54,0	1/1:0,33:8:23.93:194,24,0
LOC_Os01g62920.1	1907	.	T	C	1868.26	PASS	AC=20;AF=1.000;AN=20;DP=213;DS;Dels=0.00;HRun=1;HaplotypeScore=0.7033;MQ=57.42;MQ0=0;QD=8.77;SB=-677.68;sumGLbyD=8.98	GT:AD:DP:GQ:PL	1/1:0,21:4:11.97:98,12,0	1/1:0,22:10:24:244,24,0	1/1:0,26:3:8.99:79,9,0	1/1:0,32:10:29.99:262,30,0	1/1:0,13:4:11.94:90,12,0	1/1:0,18:12:35.93:308,36,0	1/1:0,16:7:20.95:171,21,0	1/1:0,25:2:5.96:43,6,0	1/1:0,26:19:44.96:443,45,0	1/1:0,13:7:20.96:175,21,0
LOC_Os01g62920.1	2510	.	C	G	1319.24	PASS	AC=16;AF=1.000;AN=16;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.7305;MQ=59.75;MQ0=0;QD=17.83;SB=-415.92;sumGLbyD=18.44	GT:AD:DP:GQ:PL	1/1:0,1:1:3.01:30,3,0	1/1:0,17:11:27.05:289,27,0	./.	1/1:0,2:1:3:29,3,0	1/1:0,11:8:17.98:180,18,0	1/1:0,16:11:33.01:299,33,0	1/1:0,10:9:26.98:238,27,0	./.	1/1:0,7:4:12.01:112,12,0	1/1:0,10:7:20.99:185,21,0
LOC_Os01g62920.1	2558	.	C	T	500.92	PASS	AC=12;AF=1.000;AN=12;DP=38;Dels=0.00;HRun=2;HaplotypeScore=0.1564;MQ=59.51;MQ0=0;QD=13.91;SB=-286.16;sumGLbyD=15.16	GT:AD:DP:GQ:PL	./.	1/1:0,8:6:15:146,15,0	./.	./.	1/1:0,6:4:6.02:84,6,0	1/1:0,6:5:12.02:131,12,0	1/1:0,8:5:9:108,9,0	./.	1/1:0,2:2:3.01:44,3,0	1/1:0,6:1:3:27,3,0
LOC_Os01g62920.1	2650	.	A	C	286.22	PASS	AC=8;AF=1.00;AN=8;DP=22;Dels=0.00;HRun=0;HaplotypeScore=0.3519;MQ=58.29;MQ0=0;QD=15.06;SB=-143.26;sumGLbyD=17.25	GT:AD:DP:GQ:PL	1/1:0,3:2:6:54,6,0	1/1:0,3:2:3.01:45,3,0	./.	./.	1/1:0,5:3:6.01:69,6,0	1/1:0,8:5:15.02:156,15,0	./.	./.	./.	./.
LOC_Os01g62920.1	2732	.	C	T	225.71	PASS	AC=10;AF=1.00;AN=10;DP=17;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=58.63;MQ0=0;QD=13.28;SB=-128.59;sumGLbyD=15.89	GT:AD:DP:GQ:PL	./.	1/1:0,3:3:6:67,6,0	./.	./.	1/1:0,2:2:6:54,6,0	1/1:0,5:3:6.01:70,6,0	1/1:0,2:2:3.01:44,3,0	./.	./.	1/1:0,5:1:3:29,3,0
LOC_Os12g32240.1	639	.	A	G	73.19	PASS	AC=1;AF=0.050;AN=20;DP=373;DS;Dels=0.00;HRun=0;HaplotypeScore=1.8129;MQ=36.25;MQ0=0;QD=3.85;SB=-18.69;sumGLbyD=6.05	GT:AD:DP:GQ:PL	0/0:25,0:7:20.91:0,21,163	0/0:50,0:32:95.64:0,96,746	0/1:1,18:7:2.78:113,0,3	0/0:29,0:11:32.97:0,33,282	0/0:34,0:13:38.83:0,39,297	0/0:50,0:25:74.80:0,75,604	0/0:50,0:24:71.82:0,72,580	0/0:16,0:9:26.97:0,27,227	0/0:48,2:22:41.05:0,41,458	0/0:50,0:12:35.84:0,36,272
LOC_Os12g32240.1	864	.	C	T	1432.55	PASS	AC=18;AF=1.000;AN=18;DP=333;DS;Dels=0.00;HRun=0;HaplotypeScore=1.5165;MQ=58.59;MQ0=0;QD=4.35;SB=-334.59;sumGLbyD=4.50	GT:AD:DP:GQ:PL	1/1:0,22:1:3:25,3,0	1/1:0,50:15:44.82:347,45,0	1/1:0,4:1:2.99:24,3,0	1/1:0,20:5:11.96:109,12,0	1/1:0,35:1:2.98:22,3,0	1/1:0,50:17:50.81:400,51,0	1/1:0,48:8:23.87:177,24,0	./.	1/1:0,50:13:38.85:301,39,0	1/1:0,49:3:8.97:70,9,0
LOC_Os12g32240.1	931	.	T	C	1780.48	PASS	AC=14;AF=1.000;AN=14;DP=102;DS;Dels=0.00;HRun=1;HaplotypeScore=0.9119;MQ=57.46;MQ0=0;QD=17.80;SB=-765.96;sumGLbyD=18.25	GT:AD:DP:GQ:PL	1/1:0,1:1:3:25,3,0	1/1:0,24:22:48.07:537,48,0	./.	./.	1/1:0,2:1:3:26,3,0	1/1:0,18:14:33.02:340,33,0	1/1:0,22:17:44.97:427,45,0	./.	1/1:0,16:12:24.03:265,24,0	1/1:0,16:8:23.97:202,24,0