##fileformat=VCFv4.0
##fileDate=20220901
##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/050/129/50129877/tmp/lofreq2_call_parallelyczniu8l/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_67,Description="Minimum SNV Quality (Phred) 67">
##FILTER=<ID=min_indelqual_51,Description="Minimum Indel Quality (Phred) 51">
##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60">
##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/jwd/main/050/130/50130120/outputs/galaxy_dataset_edd6311e-29d6-44ea-9c53-1de8b934c9f0.dat -csvStats /data/jwd/main/050/130/50130120/outputs/galaxy_dataset_bd832d92-3d90-4ea9-b282-63f08d89a4f1.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/d/7/9/dataset_d7970cc4-d845-4970-858e-02f7ba5eadd1.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	42184.0	PASS	AF=0.982707;DP=1330;DP4=85,104,722,585;HRUN=2;SB=20;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	49290.0	PASS	AF=0.977012;DP=1392;DP4=0,0,702,690;SB=0;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=0.987725;DP=3340;DP4=1,1,1672,1666;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	19250.0	PASS	AF=0.977230;DP=527;DP4=1,1,252,273;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	31461.0	PASS	AF=0.980210;DP=859;DP4=0,0,428,429;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	49314.0	PASS	AF=0.981888;DP=2098;DP4=0,0,1045,1051;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	32697.0	PASS	AF=0.973154;DP=894;DP4=2,3,504,385;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	4276	.	C	T	29741.0	PASS	AF=0.981949;DP=831;DP4=1,1,639,190;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	12804.0	PASS	AF=0.520703;DP=797;DP4=367,11,216,203;SB=544;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5302	.	A	G	4149.0	PASS	AF=0.116610;DP=1475;DP4=650,648,89,87;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	5628	.	C	T	28094.0	PASS	AF=0.989704;DP=777;DP4=0,0,379,398;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	14031.0	PASS	AF=0.694915;DP=590;DP4=174,0,236,179;SB=336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	49314.0	PASS	AF=0.993553;DP=1551;DP4=0,0,768,783;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	49314.0	PASS	AF=0.977535;DP=1558;DP4=0,1,793,764;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9534	.	C	T	49314.0	PASS	AF=0.984412;DP=2502;DP4=1,1,1200,1299;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	49314.0	PASS	AF=0.981550;DP=1355;DP4=2,2,734,616;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10029	.	C	T	49314.0	PASS	AF=0.945828;DP=1606;DP4=0,0,781,821;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	46438.0	PASS	AF=0.985793;DP=1267;DP4=0,0,642,625;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	33471.0	PASS	AF=0.975877;DP=912;DP4=0,0,449,462;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	33190.0	PASS	AF=0.975664;DP=904;DP4=0,0,444,455;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	11287	.	GTCTGGTTTT	G	13350.0	PASS	AF=0.997555;DP=409;DP4=29,38,202,206;HRUN=1;SB=4;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	49314.0	PASS	AF=0.974949;DP=1477;DP4=3,0,709,764;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12854	.	C	T	32749.0	PASS	AF=0.979821;DP=892;DP4=1,1,436,454;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	32911.0	PASS	AF=0.976562;DP=896;DP4=0,0,433,463;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=0.984702;DP=3007;DP4=2,3,1458,1542;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	49314.0	PASS	AF=0.978308;DP=2305;DP4=2,1,1246,1053;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	49314.0	PASS	AF=0.980050;DP=1604;DP4=0,0,796,808;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	21331.0	PASS	AF=0.975904;DP=581;DP4=2,2,289,288;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	18163	.	A	G	25394.0	PASS	AF=0.974719;DP=712;DP4=0,0,343,369;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	19955	.	C	T	49314.0	PASS	AF=0.986418;DP=2577;DP4=0,0,1302,1273;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	27353.0	PASS	AF=0.914945;DP=823;DP4=45,0,388,388;SB=128;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	34374.0	PASS	AF=0.987013;DP=924;DP4=0,0,475,449;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21618	.	C	T	49314.0	PASS	AF=0.991832;DP=2816;DP4=3,4,1412,1397;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	49314.0	PASS	AF=0.969520;DP=2395;DP4=157,157,1149,1173;HRUN=2;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21987	.	G	A	49314.0	PASS	AF=0.971223;DP=2363;DP4=4,1,1204,1153;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	37578.0	PASS	AF=0.973535;DP=1058;DP4=1,1,493,563;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	49314.0	PASS	AF=0.979866;DP=1788;DP4=1,0,898,889;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22599	.	G	C	49314.0	PASS	AF=0.984492;DP=1741;DP4=0,0,869,869;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	49314.0	PASS	AF=0.977650;DP=1745;DP4=0,0,863,879;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	49314.0	PASS	AF=0.981829;DP=1651;DP4=0,0,808,843;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22674	.	C	T	49314.0	PASS	AF=0.976661;DP=1671;DP4=0,0,814,857;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	49314.0	PASS	AF=0.980392;DP=1683;DP4=0,1,831,851;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	49314.0	PASS	AF=0.977444;DP=1596;DP4=3,2,784,805;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	49314.0	PASS	AF=0.977960;DP=1588;DP4=3,2,783,800;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22716	.	C	T	49314.0	PASS	AF=0.987611;DP=1695;DP4=1,0,852,840;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	49314.0	PASS	AF=0.866976;DP=4954;DP4=264,337,2050,2303;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22786	.	A	C	49314.0	PASS	AF=0.966713;DP=4326;DP4=8,11,1994,2310;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22792	.	C	T	49314.0	PASS	AF=0.985711;DP=4269;DP4=3,2,1982,2282;SB=1;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=0.985740;DP=4418;DP4=0,0,2060,2350;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	49314.0	PASS	AF=0.971882;DP=3023;DP4=8,10,1590,1412;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22992	.	G	A	49314.0	PASS	AF=0.984755;DP=2427;DP4=0,0,1149,1278;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	49314.0	PASS	AF=0.977565;DP=2407;DP4=1,1,1144,1261;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	49314.0	PASS	AF=0.972462;DP=2433;DP4=7,5,1146,1275;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23040	.	A	G	49314.0	PASS	AF=0.981124;DP=2437;DP4=2,1,1148,1286;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23055	.	A	G	49314.0	PASS	AF=0.979228;DP=2359;DP4=1,2,1113,1242;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	49314.0	PASS	AF=0.989863;DP=2269;DP4=0,0,1091,1177;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	49314.0	PASS	AF=0.978643;DP=2388;DP4=2,2,1173,1210;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	33624.0	PASS	AF=0.978655;DP=937;DP4=0,0,452,483;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	34230.0	PASS	AF=0.987097;DP=930;DP4=1,2,472,454;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	49314.0	PASS	AF=0.981453;DP=2588;DP4=0,0,1324,1264;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	49314.0	PASS	AF=0.981782;DP=2525;DP4=2,1,1287,1234;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23781	.	T	C	49314.0	PASS	AF=0.984828;DP=1450;DP4=2,0,697,751;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23854	.	C	A	49314.0	PASS	AF=0.975335;DP=1419;DP4=0,0,708,705;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	49314.0	PASS	AF=0.979577;DP=1420;DP4=1,1,728,689;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24424	.	A	T	49314.0	PASS	AF=0.981157;DP=3715;DP4=4,4,1876,1829;SB=0;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=0.979514;DP=3954;DP4=6,6,2000,1940;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	49314.0	PASS	AF=0.974262;DP=2370;DP4=2,2,1177,1184;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	49314.0	PASS	AF=0.978199;DP=2477;DP4=1,2,1230,1244;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	49314.0	PASS	AF=0.966142;DP=2924;DP4=1,2,1570,1348;SB=2;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=0.980381;DP=3466;DP4=2,1,1700,1759;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	45258.0	PASS	AF=0.964899;DP=1282;DP4=0,0,652,630;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	44918.0	PASS	AF=0.989274;DP=1212;DP4=1,0,615,596;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26408	.	C	T	49314.0	PASS	AF=0.954265;DP=3564;DP4=0,0,1797,1657;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26577	.	C	G	49314.0	PASS	AF=0.982902;DP=1930;DP4=1,1,933,994;SB=0;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=0.987394;DP=4125;DP4=1,0,2163,1959;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26801	.	C	T	49314.0	PASS	AF=0.980411;DP=4237;DP4=0,3,2119,2106;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	49314.0	PASS	AF=0.991272;DP=4010;DP4=2,1,1898,2106;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	27259	.	A	C	49314.0	PASS	AF=0.973996;DP=4730;DP4=11,18,2124,2568;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	48109.0	PASS	AF=0.977519;DP=1290;DP4=0,1,637,650;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	48059.0	PASS	AF=0.980408;DP=1276;DP4=0,0,631,645;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	48678.0	PASS	AF=0.985362;DP=1298;DP4=1,0,642,655;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	A	49314.0	PASS	AF=0.985457;DP=1444;DP4=0,0,724,717;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
NC_045512	27549	.	C	T	49314.0	PASS	AF=0.988926;DP=3251;DP4=0,0,1620,1630;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	49314.0	PASS	AF=0.987966;DP=1745;DP4=0,0,868,877;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=0.984275;DP=5596;DP4=3,6,2769,2811;SB=2
NC_045512	28307	.	G	A	49314.0	PASS	AF=0.977890;DP=5337;DP4=3,5,2621,2706;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.933372;DP=5178;DP4=9,4,2537,2621;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	49314.0	PASS	AF=0.836136;DP=4638;DP4=550,230,1660,2218;HRUN=2;SB=453;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	28483	.	A	G	49314.0	PASS	AF=0.967772;DP=2141;DP4=0,1,1061,1079;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512	28657	.	C	T	49314.0	PASS	AF=0.979384;DP=4511;DP4=0,0,2307,2200;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	49314.0	PASS	AF=0.983315;DP=1858;DP4=0,1,934,923;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28882	.	G	A	49314.0	PASS	AF=0.980572;DP=1853;DP4=0,0,933,920;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	49314.0	PASS	AF=0.982465;DP=1882;DP4=0,0,949,933;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=0.975827;DP=5833;DP4=1,2,2720,3107;SB=0;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=0.987166;DP=1870;DP4=377,353,741,1105;HRUN=1;SB=68;INDEL