##fileformat=VCFv4.0
##fileDate=20220927
##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/jwd01/main/050/996/50996341/tmp/lofreq2_call_parallelkbk_8g6w/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_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_59,Description="Minimum Indel Quality (Phred) 59">
##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/050/996/50996576/outputs/galaxy_dataset_7134dc8f-2717-4c53-9401-0608f3cc8edd.dat -csvStats /data/jwd01/main/050/996/50996576/outputs/galaxy_dataset_2d827137-0272-431c-b364-f79cadd4a78e.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/5/0/4/dataset_504f8e70-d9aa-40dc-bcad-7013ecb50497.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	17835.0	PASS	AF=0.981605;DP=598;DP4=54,68,369,218;HRUN=2;SB=37;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	21430.0	PASS	AF=0.938389;DP=633;DP4=2,0,307,322;SB=6;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=0.929595;DP=1605;DP4=8,8,813,769;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1059	.	C	A	2369.0	PASS	AF=0.169912;DP=565;DP4=225,228,49,63;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aAc|T265N|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	1980	.	G	T	9721.0	PASS	AF=0.913194;DP=288;DP4=0,1,152,134;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	10797.0	PASS	AF=0.928349;DP=321;DP4=0,0,158,162;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	26954.0	PASS	AF=0.964520;DP=761;DP4=1,0,374,384;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	15491.0	PASS	AF=0.960920;DP=435;DP4=1,0,269,164;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	12820.0	PASS	AF=0.867647;DP=408;DP4=0,1,309,96;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	4723.0	PASS	AF=0.432133;DP=361;DP4=193,2,83,83;SB=312;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5302	.	A	G	3100.0	PASS	AF=0.207815;DP=563;DP4=214,212,58,74;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	5628	.	C	T	11175.0	PASS	AF=0.923077;DP=338;DP4=1,1,167,168;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	5649.0	PASS	AF=0.501401;DP=357;DP4=170,0,112,75;SB=249;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	18651.0	PASS	AF=0.943503;DP=531;DP4=0,0,268,261;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	16423.0	PASS	AF=0.928425;DP=489;DP4=0,0,263,222;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9534	.	C	T	36641.0	PASS	AF=0.865435;DP=1137;DP4=0,0,546,584;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	23590.0	PASS	AF=0.955023;DP=667;DP4=2,3,389,273;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10029	.	C	T	30341.0	PASS	AF=0.925223;DP=896;DP4=2,2,410,481;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	15723.0	PASS	AF=0.899582;DP=478;DP4=0,0,252,223;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	12304.0	PASS	AF=0.913279;DP=369;DP4=0,0,178,187;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	11276.0	PASS	AF=0.841962;DP=367;DP4=5,4,176,179;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	11287	.	GTCTGGTTTT	G	6950.0	PASS	AF=0.986667;DP=225;DP4=20,19,112,110;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	18341.0	PASS	AF=0.938069;DP=549;DP4=0,0,263,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12624	.	C	A	1944.0	PASS	AF=0.175105;DP=474;DP4=158,219,47,48;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P4120H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	12854	.	C	T	10807.0	PASS	AF=0.845070;DP=355;DP4=1,6,177,171;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	12842.0	PASS	AF=0.950413;DP=363;DP4=1,1,168,192;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	42858.0	PASS	AF=0.960866;DP=1201;DP4=0,1,581,619;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	33250.0	PASS	AF=0.926577;DP=967;DP4=3,0,564,397;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
NC_045512	15714	.	C	T	18071.0	PASS	AF=0.955253;DP=514;DP4=1,0,253,260;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	7942.0	PASS	AF=0.941964;DP=224;DP4=0,1,106,116;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	10968.0	PASS	AF=0.891496;DP=341;DP4=0,0,172,165;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	44996.0	PASS	AF=0.948113;DP=1272;DP4=0,0,626,643;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	9573.0	PASS	AF=0.892256;DP=297;DP4=19,0,130,148;SB=56;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	13503.0	PASS	AF=0.931122;DP=392;DP4=0,0,215,175;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21604	.	G	T	3845.0	PASS	AF=0.164516;DP=930;DP4=377,374,89,85;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q14H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21618	.	C	T	29895.0	PASS	AF=0.867884;DP=931;DP4=1,6,462,443;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	26031.0	PASS	AF=0.982565;DP=803;DP4=44,28,379,410;HRUN=2;SB=14;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21851	.	A	C	1949.0	PASS	AF=0.289796;DP=245;DP4=87,83,38,37;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K97Q|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	21987	.	G	A	25306.0	PASS	AF=0.916340;DP=765;DP4=4,3,403,352;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	12774.0	PASS	AF=0.949062;DP=373;DP4=0,0,161,211;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	21127.0	PASS	AF=0.841727;DP=695;DP4=0,1,333,353;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	20259.0	PASS	AF=0.906710;DP=611;DP4=1,1,302,302;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	20204.0	PASS	AF=0.913540;DP=613;DP4=0,4,302,306;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22664	.	C	A	18684.0	PASS	AF=0.922101;DP=552;DP4=0,0,270,279;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	18575.0	PASS	AF=0.919065;DP=556;DP4=0,0,271,285;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	18765.0	PASS	AF=0.935484;DP=558;DP4=0,0,280,277;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	17116.0	PASS	AF=0.939335;DP=511;DP4=0,1,262,248;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	15732.0	PASS	AF=0.867735;DP=499;DP4=1,1,258,236;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22716	.	C	T	17520.0	PASS	AF=0.921722;DP=511;DP4=1,0,275,229;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=0.820296;DP=2365;DP4=149,170,1020,1022;SB=5;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=0.921507;DP=1911;DP4=3,6,948,947;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	49314.0	PASS	AF=0.950347;DP=1873;DP4=1,2,934,927;SB=2;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=0.924974;DP=1946;DP4=2,0,964,969;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22882	.	T	G	34196.0	PASS	AF=0.795763;DP=1180;DP4=7,2,635,531;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22992	.	G	A	33850.0	PASS	AF=0.923535;DP=1007;DP4=0,0,465,538;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	36099.0	PASS	AF=0.975952;DP=998;DP4=0,0,470,528;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	34866.0	PASS	AF=0.899152;DP=1061;DP4=7,7,493,550;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	33790.0	PASS	AF=0.894277;DP=1031;DP4=2,4,479,544;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	33032.0	PASS	AF=0.907646;DP=1007;DP4=0,2,475,527;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	33942.0	PASS	AF=0.947040;DP=963;DP4=0,0,464,496;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	32040.0	PASS	AF=0.894527;DP=1005;DP4=5,1,495,501;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	9001.0	PASS	AF=0.950000;DP=260;DP4=0,0,123,137;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	8188.0	PASS	AF=0.924370;DP=238;DP4=0,0,115,122;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23599	.	T	G	38741.0	PASS	AF=0.922603;DP=1137;DP4=2,2,599,528;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	36017.0	PASS	AF=0.886282;DP=1108;DP4=0,0,586,520;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	21116.0	PASS	AF=0.887195;DP=656;DP4=2,1,316,335;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23854	.	C	A	16899.0	PASS	AF=0.921260;DP=508;DP4=3,4,238,262;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	18143.0	PASS	AF=0.890311;DP=547;DP4=2,1,265,273;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	41776.0	PASS	AF=0.859435;DP=1309;DP4=1,17,665,626;SB=42;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24469	.	T	A	47759.0	PASS	AF=0.940331;DP=1391;DP4=5,1,696,688;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24821	.	G	T	49314.0	PASS	AF=0.656224;DP=2362;DP4=332,304,911,808;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Tca|A1087S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24966	.	A	G	26912.0	PASS	AF=0.887707;DP=846;DP4=2,8,377,455;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	27316.0	PASS	AF=0.939009;DP=787;DP4=0,1,369,415;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	31496.0	PASS	AF=0.852912;DP=1013;DP4=0,21,586,405;SB=80;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	38253.0	PASS	AF=0.959925;DP=1073;DP4=1,0,533,538;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	11120.0	PASS	AF=0.846995;DP=366;DP4=0,1,185,176;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26270	.	C	T	13678.0	PASS	AF=0.936387;DP=393;DP4=0,0,200,192;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	31278.0	PASS	AF=0.922118;DP=963;DP4=1,1,481,455;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	18200.0	PASS	AF=0.907407;DP=540;DP4=1,0,258,278;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	42976.0	PASS	AF=0.956703;DP=1201;DP4=0,0,635,564;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	39142.0	PASS	AF=0.947462;DP=1123;DP4=0,0,556,566;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	38024.0	PASS	AF=0.947761;DP=1072;DP4=1,0,489,576;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	27259	.	A	C	47862.0	PASS	AF=0.806818;DP=1760;DP4=100,107,630,913;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	13532.0	PASS	AF=0.905707;DP=403;DP4=0,0,202,196;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	12580.0	PASS	AF=0.854220;DP=391;DP4=1,1,200,187;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	12931.0	PASS	AF=0.870558;DP=394;DP4=4,0,200,190;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	A	15550.0	PASS	AF=0.961009;DP=436;DP4=0,0,227,208;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	36336.0	PASS	AF=0.892040;DP=1093;DP4=0,0,540,542;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	11735.0	PASS	AF=0.923754;DP=341;DP4=0,0,173,164;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=0.924107;DP=1568;DP4=3,14,792,754;SB=21
NC_045512	28307	.	G	A	46522.0	PASS	AF=0.822322;DP=1559;DP4=2,0,766,752;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28311	.	C	T	43345.0	PASS	AF=0.783117;DP=1540;DP4=3,29,764,739;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	35243.0	PASS	AF=0.759166;DP=1391;DP4=263,96,409,647;HRUN=2;SB=293;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	9278.0	PASS	AF=0.504092;DP=611;DP4=0,6,165,174;SB=15;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512	28483	.	A	T	6655.0	PASS	AF=0.386252;DP=611;DP4=0,6,130,136;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q70H|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28657	.	C	T	49314.0	PASS	AF=0.912524;DP=1589;DP4=7,8,902,653;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	21838.0	PASS	AF=0.978003;DP=591;DP4=0,0,297,294;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	20034.0	PASS	AF=0.919932;DP=587;DP4=0,0,294,292;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	20532.0	PASS	AF=0.931667;DP=600;DP4=0,0,300,297;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=0.902601;DP=1653;DP4=2,1,735,914;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	27833.0	PASS	AF=0.994203;DP=690;DP4=128,105,232,454;HRUN=1;SB=77;INDEL