##fileformat=VCFv4.0
##fileDate=20220906
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd/main/050/269/50269466/tmp/lofreq2_call_parallelbsw9y3ln/0.vcf.gz reads.bam 
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58">
##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269701/outputs/galaxy_dataset_ef5dc3b4-139d-4ea2-92d6-0eee2b2185ce.dat -csvStats /data/jwd01/main/050/269/50269701/outputs/galaxy_dataset_e009b109-f15c-434d-af07-16d0fbe31d3c.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/f/0/8/dataset_f08a98f8-5b31-4629-83fd-0bc9698a48ac.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
NC_045512	509	.	GGTCATGTTA	G	44081.0	PASS	AF=0.977320;DP=1455;DP4=71,87,803,619;HRUN=2;SB=21;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	670	.	T	G	28402.0	PASS	AF=0.924065;DP=856;DP4=2,1,417,436;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	900	.	C	T	49314.0	PASS	AF=0.949196;DP=1555;DP4=0,0,790,764;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1980	.	G	T	12662.0	PASS	AF=0.872774;DP=393;DP4=2,1,193,195;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	23573.0	PASS	AF=0.950599;DP=668;DP4=1,0,337,328;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	3037	.	C	T	28907.0	PASS	AF=0.959559;DP=816;DP4=0,0,402,413;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	9720.0	PASS	AF=0.929329;DP=283;DP4=0,0,153,129;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	4276	.	C	T	14067.0	PASS	AF=0.935644;DP=404;DP4=2,0,271,131;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	11408.0	PASS	AF=0.787589;DP=419;DP4=70,2,176,171;SB=153;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	8379.0	PASS	AF=0.702312;DP=346;DP4=80,0,164,100;SB=136;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	26816.0	PASS	AF=0.952191;DP=753;DP4=0,0,369,375;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9424	.	A	G	25123.0	PASS	AF=0.950207;DP=723;DP4=0,1,356,364;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9495	.	T	C	24939.0	PASS	AF=0.798876;DP=890;DP4=12,102,395,380;SB=171;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
NC_045512	9534	.	C	T	36433.0	PASS	AF=0.945894;DP=1035;DP4=1,1,363,670;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9866	.	C	T	18660.0	PASS	AF=0.938889;DP=540;DP4=3,3,316,216;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10029	.	C	T	29070.0	PASS	AF=0.902746;DP=874;DP4=3,3,586,282;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	27766.0	PASS	AF=0.922030;DP=808;DP4=1,1,413,392;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	16235.0	PASS	AF=0.908714;DP=482;DP4=1,1,246,232;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	16642.0	PASS	AF=0.910180;DP=501;DP4=1,2,258,240;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	11287	.	GTCTGGTTTT	G	10180.0	PASS	AF=0.990991;DP=333;DP4=26,17,169,161;HRUN=1;SB=5;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	24427.0	PASS	AF=0.913514;DP=740;DP4=0,0,352,382;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12854	.	C	T	14545.0	PASS	AF=0.905530;DP=434;DP4=1,2,228,202;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	15074.0	PASS	AF=0.959716;DP=422;DP4=0,0,211,209;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	49314.0	PASS	AF=0.942193;DP=1505;DP4=0,0,711,788;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	15451	.	G	A	29209.0	PASS	AF=0.851222;DP=941;DP4=1,1,518,419;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
NC_045512	15714	.	C	T	27739.0	PASS	AF=0.955243;DP=782;DP4=0,1,378,401;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	12584.0	PASS	AF=0.899736;DP=379;DP4=0,1,192,183;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	18163	.	A	G	16936.0	PASS	AF=0.931507;DP=511;DP4=1,0,247,260;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	19955	.	C	T	41409.0	PASS	AF=0.948936;DP=1175;DP4=0,0,609,564;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	20055	.	A	G	8915.0	PASS	AF=0.880866;DP=277;DP4=17,0,116,143;SB=56;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	10033.0	PASS	AF=0.916107;DP=298;DP4=1,0,179,113;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21441	.	T	C	19924.0	PASS	AF=0.894569;DP=626;DP4=9,8,346,263;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S7064|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
NC_045512	21618	.	C	T	45561.0	PASS	AF=0.910189;DP=1325;DP4=1,0,618,685;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	42692.0	PASS	AF=0.986760;DP=1284;DP4=40,19,574,693;HRUN=2;SB=31;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21773	.	T	C	10733.0	PASS	AF=0.922601;DP=323;DP4=2,2,146,172;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S71P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	21987	.	G	A	34993.0	PASS	AF=0.787603;DP=1210;DP4=7,0,669,526;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	23440.0	PASS	AF=0.945827;DP=683;DP4=0,0,284,396;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22578	.	G	A	31260.0	PASS	AF=0.876152;DP=977;DP4=1,0,462,510;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22599	.	G	C	32998.0	PASS	AF=0.953813;DP=931;DP4=0,0,437,491;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22629	.	A	C	27981.0	PASS	AF=0.895540;DP=852;DP4=0,0,405,445;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22664	.	C	A	24854.0	PASS	AF=0.891247;DP=754;DP4=3,1,325,424;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22674	.	C	T	21228.0	PASS	AF=0.806540;DP=734;DP4=0,1,306,426;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22679	.	T	C	24327.0	PASS	AF=0.947592;DP=706;DP4=0,0,294,410;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22686	.	C	T	19403.0	PASS	AF=0.858915;DP=645;DP4=0,2,271,370;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	19658.0	PASS	AF=0.885950;DP=605;DP4=1,0,255,349;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22716	.	C	T	17060.0	PASS	AF=0.964135;DP=474;DP4=0,0,218,256;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22775	.	G	A	27032.0	PASS	AF=0.759106;DP=1208;DP4=110,126,463,508;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22786	.	A	C	38537.0	PASS	AF=0.878986;DP=1223;DP4=3,6,600,609;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22792	.	C	T	42345.0	PASS	AF=0.900631;DP=1268;DP4=1,3,633,628;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22813	.	G	T	49314.0	PASS	AF=0.890789;DP=1520;DP4=2,1,791,723;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22882	.	T	G	41212.0	PASS	AF=0.893515;DP=1249;DP4=6,4,704,533;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22992	.	G	A	41603.0	PASS	AF=0.922204;DP=1234;DP4=6,8,527,682;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22995	.	C	A	44039.0	PASS	AF=0.955538;DP=1237;DP4=0,1,538,695;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23013	.	A	C	39440.0	PASS	AF=0.865539;DP=1242;DP4=7,8,527,697;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23040	.	A	G	36321.0	PASS	AF=0.893789;DP=1111;DP4=3,2,482,622;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23055	.	A	G	32481.0	PASS	AF=0.900802;DP=998;DP4=3,0,450,542;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	34000.0	PASS	AF=0.937628;DP=978;DP4=3,4,450,521;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23075	.	T	C	29355.0	PASS	AF=0.894168;DP=926;DP4=4,3,455,462;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	12242.0	PASS	AF=0.927419;DP=372;DP4=0,0,162,210;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23525	.	C	T	9334.0	PASS	AF=0.890071;DP=282;DP4=2,1,135,144;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23599	.	T	G	34424.0	PASS	AF=0.939394;DP=990;DP4=1,0,523,466;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23604	.	C	A	32027.0	PASS	AF=0.885396;DP=986;DP4=3,0,515,468;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23854	.	C	A	20408.0	PASS	AF=0.932432;DP=592;DP4=1,2,284,305;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23948	.	G	T	29879.0	PASS	AF=0.920507;DP=868;DP4=1,2,443,419;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24424	.	A	T	47659.0	PASS	AF=0.901191;DP=1427;DP4=2,14,769,642;SB=31;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24469	.	T	A	49314.0	PASS	AF=0.939541;DP=1654;DP4=2,0,884,763;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	33803.0	PASS	AF=0.894434;DP=1042;DP4=3,1,460,569;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	32268.0	PASS	AF=0.937773;DP=916;DP4=0,1,455,455;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	42188.0	PASS	AF=0.841246;DP=1348;DP4=2,8,756,578;SB=16;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	49314.0	PASS	AF=0.957550;DP=1437;DP4=0,2,737,694;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	25026.0	PASS	AF=0.914667;DP=750;DP4=3,2,391,352;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26270	.	C	T	31607.0	PASS	AF=0.924342;DP=912;DP4=0,1,470,440;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26324	.	T	C	2986.0	PASS	AF=0.146732;DP=811;DP4=353,331,66,57;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L27S|75|E|protein_coding|CODING|GU280_gp04|1|C)
NC_045512	26333	.	C	T	20679.0	PASS	AF=0.768638;DP=778;DP4=71,56,346,305;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26550	.	G	A	4831.0	PASS	AF=0.223039;DP=816;DP4=308,306,100,101;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V10I|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26577	.	C	G	31868.0	PASS	AF=0.906152;DP=959;DP4=0,1,489,466;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512	26709	.	G	A	49314.0	PASS	AF=0.920627;DP=2041;DP4=3,3,994,1025;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26728	.	C	T	5102.0	PASS	AF=0.110196;DP=1942;DP4=855,852,118,113;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A69V|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26801	.	C	T	49314.0	PASS	AF=0.887376;DP=1616;DP4=4,4,765,828;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	27420.0	PASS	AF=0.846238;DP=917;DP4=15,20,417,458;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26985	.	C	T	12028.0	PASS	AF=0.361871;DP=1133;DP4=334,325,236,233;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H155Y|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	27259	.	A	C	49314.0	PASS	AF=0.883410;DP=2170;DP4=6,12,916,1230;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	24097.0	PASS	AF=0.903090;DP=712;DP4=0,0,351,357;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27383	.	A	T	23587.0	PASS	AF=0.887006;DP=708;DP4=0,0,351,353;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512	27384	.	T	C	24162.0	PASS	AF=0.898187;DP=717;DP4=0,0,355,359;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	T	29456.0	PASS	AF=0.954654;DP=838;DP4=1,1,402,428;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27549	.	C	T	49314.0	PASS	AF=0.900465;DP=2150;DP4=0,0,1090,1037;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	33703.0	PASS	AF=0.934827;DP=982;DP4=2,3,465,505;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512	28271	.	A	T	49314.0	PASS	AF=0.878304;DP=1627;DP4=1,15,781,826;SB=32
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.812185;DP=1986;DP4=5,15,972,988;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	36912.0	PASS	AF=0.764169;DP=1535;DP4=239,128,540,633;HRUN=2;SB=97;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
NC_045512	28657	.	C	T	49314.0	PASS	AF=0.882603;DP=2828;DP4=5,5,1516,1283;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	44587.0	PASS	AF=0.945774;DP=1254;DP4=0,1,574,678;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28882	.	G	A	42098.0	PASS	AF=0.911788;DP=1247;DP4=0,2,570,668;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	42990.0	PASS	AF=0.922586;DP=1253;DP4=0,0,570,681;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29510	.	A	C	49314.0	PASS	AF=0.922913;DP=2815;DP4=12,12,1232,1545;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.989508;DP=1239;DP4=124,107,440,786;HRUN=1;SB=61;INDEL