##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/050/996/50996342/tmp/lofreq2_call_parallelr6xd9css/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_53,Description="Minimum Indel Quality (Phred) 53">
##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75">
##FILTER=<ID=min_indelqual_61,Description="Minimum Indel Quality (Phred) 61">
##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/050/996/50996577/outputs/galaxy_dataset_c1fe9188-61a8-4620-a5e5-b8767f365e04.dat -csvStats /data/jwd01/main/050/996/50996577/outputs/galaxy_dataset_1a8b9f67-27f7-485f-930a-8cc569fda1e0.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/a/b/0/dataset_ab07b6bf-259d-40b7-b62a-5a146ab70f14.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	20818.0	PASS	AF=0.848225;DP=817;DP4=122,112,431,262;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	21209.0	PASS	AF=0.911628;DP=645;DP4=1,0,304,336;SB=3;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=0.943702;DP=2096;DP4=1,1,1114,977;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	13514.0	PASS	AF=0.879518;DP=415;DP4=3,0,215,194;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	20107.0	PASS	AF=0.919328;DP=595;DP4=0,0,295,299;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	28270.0	PASS	AF=0.950125;DP=802;DP4=0,0,369,431;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	19564.0	PASS	AF=0.953069;DP=554;DP4=1,0,348,205;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	14879.0	PASS	AF=0.812623;DP=507;DP4=2,1,351,147;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	10608.0	PASS	AF=0.699552;DP=446;DP4=113,1,162,170;SB=268;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	3284.0	PASS	AF=0.258427;DP=445;DP4=318,1,77,49;SB=287;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	7085	.	A	G	7084.0	PASS	AF=0.198809;DP=1343;DP4=512,520,152,138;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T2274A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9344	.	C	T	30690.0	PASS	AF=0.933782;DP=891;DP4=0,0,461,423;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	31617.0	PASS	AF=0.924488;DP=927;DP4=0,0,493,424;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9495	.	T	C	31844.0	PASS	AF=0.882353;DP=986;DP4=2,28,509,445;SB=67;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
NC_045512	9534	.	C	T	36963.0	PASS	AF=0.812550;DP=1243;DP4=0,1,435,790;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	28044.0	PASS	AF=0.944376;DP=809;DP4=3,1,478,324;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	22775.0	PASS	AF=0.880450;DP=711;DP4=0,1,413,295;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	29355.0	PASS	AF=0.907029;DP=882;DP4=0,2,462,412;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	9980.0	PASS	AF=0.880259;DP=309;DP4=1,0,142,163;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	9236.0	PASS	AF=0.828947;DP=304;DP4=4,6,140,153;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	3861.0	PASS	AF=1.000000;DP=124;DP4=4,3,61,63;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	14354.0	PASS	AF=0.936768;DP=427;DP4=1,1,194,228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12342	.	C	T	13753.0	PASS	AF=0.357642;DP=1289;DP4=575,202,313,196;SB=55;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4026I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12854	.	C	T	9938.0	PASS	AF=0.840125;DP=319;DP4=0,5,154,158;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	11413.0	PASS	AF=0.980707;DP=311;DP4=0,0,143,167;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	13859	.	A	G	1972.0	PASS	AF=0.149446;DP=542;DP4=234,212,42,50;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D4537G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	14408	.	C	T	49314.0	PASS	AF=0.967153;DP=1644;DP4=3,2,792,845;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	14724	.	C	T	18069.0	PASS	AF=0.457478;DP=1364;DP4=361,349,345,305;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F4825|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	15451	.	G	A	49314.0	PASS	AF=0.943262;DP=1551;DP4=0,2,915,631;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
NC_045512	15714	.	C	T	28421.0	PASS	AF=0.968314;DP=789;DP4=0,0,392,395;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	15217.0	PASS	AF=0.870293;DP=478;DP4=0,2,219,250;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	18163	.	A	G	21071.0	PASS	AF=0.878788;DP=660;DP4=1,0,321,333;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	18486	.	C	T	1673.0	PASS	AF=0.175676;DP=370;DP4=141,154,40,33;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L6079|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	19955	.	C	T	49314.0	PASS	AF=0.940071;DP=2553;DP4=2,3,1202,1341;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	12803.0	PASS	AF=0.861575;DP=419;DP4=44,1,182,192;SB=112;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	21961.0	PASS	AF=0.945687;DP=626;DP4=0,0,351,275;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21441	.	T	C	8700.0	PASS	AF=0.429825;DP=684;DP4=203,161,174,143;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S7064|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
NC_045512	21618	.	C	T	48579.0	PASS	AF=0.847995;DP=1546;DP4=0,4,717,805;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	43279.0	PASS	AF=0.981413;DP=1345;DP4=75,54,591,729;HRUN=2;SB=23;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	4329.0	PASS	AF=0.403846;DP=364;DP4=97,105,73,89;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S71P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	21987	.	G	A	42165.0	PASS	AF=0.924071;DP=1238;DP4=2,0,692,539;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	25623.0	PASS	AF=0.942971;DP=754;DP4=2,0,337,415;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22578	.	G	A	24366.0	PASS	AF=0.859649;DP=798;DP4=2,1,398,386;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	23033.0	PASS	AF=0.874483;DP=725;DP4=0,0,372,343;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	24122.0	PASS	AF=0.870180;DP=778;DP4=0,5,393,377;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22664	.	C	A	24852.0	PASS	AF=0.918367;DP=735;DP4=0,0,354,377;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	24962.0	PASS	AF=0.925134;DP=748;DP4=0,0,355,390;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	24338.0	PASS	AF=0.905711;DP=753;DP4=0,0,361,390;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	22895.0	PASS	AF=0.935622;DP=699;DP4=2,1,332,361;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	20503.0	PASS	AF=0.845113;DP=665;DP4=1,3,317,337;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22716	.	C	T	24283.0	PASS	AF=0.932203;DP=708;DP4=1,2,340,363;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=0.641449;DP=4719;DP4=730,779,1673,1531;SB=18;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=0.909284;DP=2822;DP4=9,19,1461,1330;SB=14;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=0.948333;DP=2729;DP4=0,2,1429,1292;SB=6;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=0.924780;DP=2845;DP4=2,3,1482,1350;SB=1;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=0.768566;DP=1966;DP4=6,4,1092,856;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	49314.0	PASS	AF=0.924841;DP=1570;DP4=2,1,687,869;SB=2;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=0.975765;DP=1568;DP4=1,1,705,858;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=0.897420;DP=1628;DP4=7,8,719,884;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	49314.0	PASS	AF=0.909502;DP=1547;DP4=2,4,693,844;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	48995.0	PASS	AF=0.905459;DP=1502;DP4=1,3,682,808;SB=2;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=0.950538;DP=1395;DP4=0,0,658,737;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	48140.0	PASS	AF=0.894947;DP=1504;DP4=9,0,731,764;SB=27;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	15329.0	PASS	AF=0.954442;DP=439;DP4=0,0,206,230;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	11580.0	PASS	AF=0.895184;DP=353;DP4=0,0,178,172;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	49314.0	PASS	AF=0.919446;DP=1589;DP4=4,0,833,746;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23604	.	C	A	49013.0	PASS	AF=0.877457;DP=1526;DP4=2,1,798,717;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23854	.	C	A	21886.0	PASS	AF=0.898827;DP=682;DP4=2,3,317,360;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	26172.0	PASS	AF=0.900000;DP=780;DP4=0,0,377,398;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=0.851435;DP=1777;DP4=1,33,902,840;SB=90;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=0.929825;DP=1881;DP4=6,0,948,922;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	29654.0	PASS	AF=0.887689;DP=926;DP4=0,5,426,490;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	30021.0	PASS	AF=0.927918;DP=874;DP4=0,0,416,456;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	40468.0	PASS	AF=0.833333;DP=1320;DP4=1,27,756,534;SB=89;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=0.966743;DP=1744;DP4=0,0,928,814;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	23747.0	PASS	AF=0.858257;DP=769;DP4=1,0,374,391;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	24266.0	PASS	AF=0.901389;DP=720;DP4=0,1,367,350;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26333	.	C	T	22038.0	PASS	AF=0.905465;DP=677;DP4=0,0,355,316;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26577	.	C	G	15659.0	PASS	AF=0.896480;DP=483;DP4=0,0,235,241;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512	26625	.	C	T	7705.0	PASS	AF=0.469582;DP=526;DP4=129,140,120,135;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L35|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26709	.	G	A	49314.0	PASS	AF=0.951613;DP=1736;DP4=1,1,973,756;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26754	.	G	A	7424.0	PASS	AF=0.164614;DP=1786;DP4=801,659,174,140;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G78S|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26801	.	C	T	49314.0	PASS	AF=0.938865;DP=1603;DP4=1,1,827,761;SB=0;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=0.953297;DP=1456;DP4=0,0,662,780;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26985	.	C	T	13083.0	PASS	AF=0.387238;DP=1144;DP4=326,325,247,243;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=0.901447;DP=2212;DP4=3,5,872,1321;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	8676.0	PASS	AF=0.881679;DP=262;DP4=0,0,129,131;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	8693.0	PASS	AF=0.888462;DP=260;DP4=0,0,128,130;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	9016.0	PASS	AF=0.906367;DP=267;DP4=1,0,133,133;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	T	11248.0	PASS	AF=0.939577;DP=331;DP4=1,0,175,155;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=0.902861;DP=1503;DP4=0,1,805,675;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	25681.0	PASS	AF=0.934404;DP=747;DP4=0,0,381,365;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=0.942808;DP=2308;DP4=2,17,1245,1043;SB=39
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.826858;DP=2368;DP4=7,39,1228,1089;SB=66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	48102.0	PASS	AF=0.725214;DP=1987;DP4=462,121,520,921;HRUN=2;SB=713;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=0.915625;DP=2240;DP4=0,1,1299,920;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	25064.0	PASS	AF=0.958153;DP=693;DP4=0,0,323,368;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	22700.0	PASS	AF=0.885341;DP=689;DP4=1,0,318,366;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	23625.0	PASS	AF=0.920228;DP=702;DP4=2,0,324,371;SB=6;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=0.885417;DP=2304;DP4=5,1,1010,1280;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	30870.0	PASS	AF=0.989501;DP=762;DP4=116,100,235,519;HRUN=1;SB=84;INDEL