##fileformat=VCFv4.0
##fileDate=20221107
##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/051/983/51983886/tmp/lofreq2_call_parallel739h_0kf/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_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/051/984/51984231/outputs/galaxy_dataset_2a6dc736-1c58-4b90-a56b-3c41b5b241ad.dat -csvStats /data/jwd01/main/051/984/51984231/outputs/galaxy_dataset_a3db7d9d-012b-4774-8ac9-298af3edbf29.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/f/4/0/dataset_f402fbb5-67b8-463c-a425-3fd5d921cfdb.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	49314.0	PASS	AF=0.991453;DP=1638;DP4=78,102,891,733;HRUN=2;SB=24;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	49314.0	PASS	AF=0.936671;DP=1658;DP4=0,1,818,837;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=0.963995;DP=2944;DP4=0,0,1497,1442;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	11162.0	PASS	AF=0.920000;DP=325;DP4=2,1,151,170;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	32452.0	PASS	AF=0.949134;DP=924;DP4=0,0,467,454;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=0.947160;DP=1514;DP4=0,0,751,753;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	30094.0	PASS	AF=0.946387;DP=858;DP4=1,1,504,349;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	36928.0	PASS	AF=0.956772;DP=1041;DP4=1,0,699,339;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	25367.0	PASS	AF=0.732809;DP=1018;DP4=207,8,412,388;SB=398;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5302	.	A	G	22744.0	PASS	AF=0.476312;DP=1562;DP4=406,385,386,382;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	5628	.	C	T	33093.0	PASS	AF=0.967161;DP=944;DP4=2,1,464,477;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	18176.0	PASS	AF=0.551521;DP=1019;DP4=415,0,341,260;SB=723;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	38314.0	PASS	AF=0.961718;DP=1071;DP4=0,0,532,537;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	32921.0	PASS	AF=0.938797;DP=964;DP4=0,1,477,483;SB=0;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=0.951883;DP=1912;DP4=0,0,952,953;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	41117.0	PASS	AF=0.943364;DP=1183;DP4=0,0,632,546;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=0.917537;DP=1819;DP4=1,1,874,935;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	42686.0	PASS	AF=0.946414;DP=1213;DP4=0,0,616,594;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	34188.0	PASS	AF=0.929293;DP=990;DP4=0,0,489,499;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	33538.0	PASS	AF=0.913968;DP=988;DP4=1,1,489,494;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	14876.0	PASS	AF=0.981289;DP=481;DP4=32,39,234,238;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	41955.0	PASS	AF=0.926772;DP=1270;DP4=1,1,633,631;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	13590.0	PASS	AF=0.375369;DP=1356;DP4=381,440,250,283;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P4120H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	12854	.	C	T	28796.0	PASS	AF=0.926506;DP=830;DP4=1,1,403,422;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	29279.0	PASS	AF=0.946860;DP=828;DP4=0,0,397,428;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=0.951433;DP=2512;DP4=1,1,1232,1273;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=0.917309;DP=1947;DP4=20,20,1022,883;SB=1;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=0.947186;DP=1439;DP4=0,0,709,724;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	16915	.	C	T	2734.0	PASS	AF=0.133886;DP=844;DP4=342,376,58,66;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L5556|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	19215.0	PASS	AF=0.938406;DP=552;DP4=0,0,269,280;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	15895.0	PASS	AF=0.924843;DP=479;DP4=1,1,239,238;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=0.943801;DP=2847;DP4=1,0,1468,1375;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	26271.0	PASS	AF=0.905000;DP=800;DP4=25,2,382,389;SB=53;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	11109.0	PASS	AF=0.928349;DP=321;DP4=0,0,165,154;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=0.958054;DP=2384;DP4=0,0,1161,1218;SB=0;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=0.979592;DP=2156;DP4=73,71,1008,1104;HRUN=2;SB=3;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	4638.0	PASS	AF=0.285217;DP=575;DP4=201,194,91,88;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	49314.0	PASS	AF=0.912939;DP=2079;DP4=1,2,1084,985;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	37598.0	PASS	AF=0.928826;DP=1124;DP4=4,0,516,602;SB=13;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=0.929839;DP=2366;DP4=5,5,1155,1192;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=0.954260;DP=2230;DP4=0,0,1094,1131;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=0.949074;DP=2160;DP4=0,1,1062,1095;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=0.940941;DP=1998;DP4=2,1,962,1029;SB=2;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=0.931911;DP=1968;DP4=0,0,919,1041;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=0.927711;DP=1909;DP4=1,1,907,995;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=0.940745;DP=1772;DP4=1,2,855,907;SB=0;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=0.917285;DP=1753;DP4=1,0,854,892;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	49314.0	PASS	AF=0.939832;DP=1662;DP4=1,0,839,819;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=0.546070;DP=5166;DP4=1022,1217,1310,1612;SB=2;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=0.902530;DP=3201;DP4=4,15,1426,1748;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=0.953403;DP=3262;DP4=0,0,1467,1793;SB=0;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=0.957267;DP=3557;DP4=0,3,1634,1915;SB=5;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=0.927554;DP=2457;DP4=3,5,1261,1185;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=0.961011;DP=2334;DP4=0,0,1125,1199;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=0.951303;DP=2341;DP4=0,3,1136,1201;SB=6;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=0.919054;DP=2409;DP4=11,12,1145,1237;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=0.934744;DP=2268;DP4=2,2,1075,1185;SB=0;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=0.923112;DP=2185;DP4=1,4,1048,1127;SB=4;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=0.970673;DP=2080;DP4=0,0,1009,1070;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=0.924171;DP=2110;DP4=1,1,1034,1072;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	17452.0	PASS	AF=0.944554;DP=505;DP4=0,0,249,254;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	15743.0	PASS	AF=0.921569;DP=459;DP4=0,0,219,239;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=0.936208;DP=1693;DP4=1,2,868,820;SB=2;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=0.948901;DP=1683;DP4=1,1,864,817;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	48027.0	PASS	AF=0.939855;DP=1380;DP4=1,3,684,689;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	38813.0	PASS	AF=0.944593;DP=1119;DP4=0,2,553,558;SB=3;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=0.951482;DP=1484;DP4=0,0,752,729;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=0.939243;DP=3012;DP4=3,8,1569,1427;SB=8;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=0.933240;DP=3580;DP4=4,1,1833,1737;SB=4;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=0.443133;DP=5337;DP4=1396,1351,1294,1272;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	49314.0	PASS	AF=0.915657;DP=2229;DP4=1,4,1078,1118;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	49314.0	PASS	AF=0.941489;DP=2068;DP4=1,2,1046,1013;SB=2;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=0.889061;DP=2578;DP4=4,4,1376,1190;SB=0;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=0.944794;DP=2862;DP4=1,1,1439,1419;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	42512.0	PASS	AF=0.922109;DP=1271;DP4=1,0,616,646;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	48617.0	PASS	AF=0.956458;DP=1355;DP4=1,0,691,661;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=0.940901;DP=2775;DP4=1,0,1395,1339;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=0.927210;DP=1731;DP4=1,2,842,853;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=0.940457;DP=3107;DP4=1,2,1566,1529;SB=2;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=0.944444;DP=3312;DP4=1,0,1635,1671;SB=3;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=0.959469;DP=2862;DP4=1,1,1379,1474;SB=0;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=0.921806;DP=3632;DP4=13,19,1694,1891;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	41385.0	PASS	AF=0.929780;DP=1182;DP4=0,0,575,603;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	41295.0	PASS	AF=0.931624;DP=1170;DP4=2,2,566,595;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	41493.0	PASS	AF=0.926520;DP=1184;DP4=1,0,575,600;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	A	49154.0	PASS	AF=0.936924;DP=1411;DP4=1,1,720,687;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=0.955828;DP=3509;DP4=0,0,1775,1729;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=0.949483;DP=1742;DP4=1,2,854,880;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=0.938697;DP=3915;DP4=1,14,1939,1948;SB=30
NC_045512	28307	.	G	A	49314.0	PASS	AF=0.898558;DP=3953;DP4=1,7,1945,1961;SB=11;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=0.823724;DP=3937;DP4=14,32,1925,1937;SB=19;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=0.793943;DP=3203;DP4=417,273,1123,1420;HRUN=2;SB=134;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=0.844926;DP=1754;DP4=0,2,808,788;SB=6;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=0.923977;DP=3933;DP4=1,2,2032,1877;SB=2;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=0.941981;DP=1827;DP4=0,1,899,925;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	49314.0	PASS	AF=0.932343;DP=1818;DP4=1,3,887,918;SB=2;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=0.947425;DP=1864;DP4=1,0,913,948;SB=3;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=0.942881;DP=4867;DP4=0,4,2265,2597;SB=8;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=0.988372;DP=1634;DP4=307,325,681,934;HRUN=1;SB=22;INDEL