view test-data/1085080.vcf @ 3:3d0adeee3f2b draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit c062eb1cd00ce9d565f3e2f3b042b3dd90d78ce4"

##fileformat=VCFv4.0
##fileDate=20201106
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --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 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb03/galaxy_db/job_working_directory/012/246/12246261/tmp/lofreq2_call_parallelpau7d8kw/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_76,Description="Minimum SNV Quality (Phred) 76">
##FILTER=<ID=min_indelqual_61,Description="Minimum Indel Quality (Phred) 61">
##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80">
##FILTER=<ID=min_indelqual_65,Description="Minimum Indel Quality (Phred) 65">
##FILTER=<ID=min_af_0.050000,Description="Minimum allele frequency 0.050000">
##FILTER=<ID=min_dp_5,Description="Minimum Coverage 5">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/dnb03/galaxy_db/job_working_directory/012/246/12246328/outputs/galaxy_dataset_1054f879-0756-4754-86b9-66ab53b4f190.dat NC_045512.2 /data/dnb03/galaxy_db/files/9/8/a/dataset_98aa5c97-caf5-43bb-8d6e-033816a165dc.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_045512.2	186	.	C	T	134.0	min_af_0.050000	AF=0.002111;DP=9950;DP4=7060,2864,14,8;SB=3
NC_045512.2	241	.	C	T	49314.0	PASS	AF=0.991085;DP=4711;DP4=0,2,2421,2286;SB=6
NC_045512.2	295	.	GA	G	86.0	min_af_0.050000	AF=0.000776;DP=12892;DP4=2790,10130,3,7;HRUN=4;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aca/|T12|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aca/|T12|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	320	.	C	T	130.0	min_af_0.050000	AF=0.001651;DP=12717;DP4=2676,10012,6,18;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P19S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2	343	.	G	A	85.0	min_af_0.050000	AF=0.000997;DP=20063;DP4=9201,10833,11,13;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V26|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2	346	.	C	T	87.0	min_af_0.050000	AF=0.000947;DP=20061;DP4=9173,10861,6,14;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L27|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2	384	.	C	T	113.0	min_af_0.050000	AF=0.001059;DP=19826;DP4=8681,11111,8,18;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|T|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S40L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T)
NC_045512.2	408	.	A	G	92.0	min_af_0.050000	AF=0.001520;DP=9869;DP4=7607,2236,8,7;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D48G|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G)
NC_045512.2	439	.	A	G	136.0	min_af_0.050000	AF=0.003018;DP=9942;DP4=7528,2377,22,11;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K58|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G)
NC_045512.2	443	.	GT	G	152.0	min_af_0.050000	AF=0.001419;DP=9867;DP4=7517,2353,10,4;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/|L61|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|G|WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttg/|L61|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	645	.	G	A	139.0	min_af_0.050000	AF=0.001901;DP=9469;DP4=1920,7528,7,13;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G127D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2	685	.	AAAGTCATTT	A	483.0	min_af_0.050000	AF=0.003415;DP=9662;DP4=2267,7379,9,24;HRUN=3;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||aagtcattt/|KSF141|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009725297.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|179|ORF1ab|protein_coding|CODING|YP_009742608.1|1|A|WARNING_TRANSCRIPT_NO_STOP_CODON),CODON_DELETION(MODERATE||aagtcattt/|KSF141|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A)
NC_045512.2	1019	.	C	T	99.0	min_af_0.050000	AF=0.001342;DP=11174;DP4=9196,1955,12,3;SB=1;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q252*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q72*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2	1075	.	T	C	87.0	min_af_0.050000	AF=0.001237;DP=11322;DP4=9045,2250,18,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C270|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C270|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C90|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C90|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1115	.	A	T	412.0	min_af_0.050000	AF=0.008698;DP=3449;DP4=1366,2051,2,29;SB=42;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I284F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Ttt|I104F|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1133	.	A	T	223.0	min_af_0.050000	AF=0.005443;DP=3491;DP4=1491,1981,17,2;SB=42;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K290*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K110*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2	1224	.	T	C	100.0	min_af_0.050000	AF=0.001457;DP=10296;DP4=1820,8452,7,12;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L320P|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L320P|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L140P|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cCc|L140P|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1304	.	G	T	221.0	min_af_0.050000	AF=0.002447;DP=10217;DP4=1929,8259,6,19;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E347*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E347*|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E167*|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Gag/Tag|E167*|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2	1644	.	A	C	80.0	min_af_0.050000	AF=0.001682;DP=7133;DP4=5888,1231,7,5;SB=13;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N460T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N280T|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1647	.	T	A	91.0	min_af_0.050000	AF=0.001680;DP=7142;DP4=5854,1271,8,5;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I461N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aAc|I281N|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1656	.	T	A	90.0	min_af_0.050000	AF=0.001807;DP=7195;DP4=5827,1352,9,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V464D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V284D|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1695	.	T	G	82.0	min_af_0.050000	AF=0.002029;DP=7394;DP4=5871,1505,11,5;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L477W|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L477W|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L297W|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tGg|L297W|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1702	.	T	C	195.0	min_af_0.050000	AF=0.003394;DP=7366;DP4=5832,1483,22,5;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S479|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S299|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	1914	.	G	A	150.0	min_af_0.050000	AF=0.002571;DP=6613;DP4=1088,5503,6,12;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R550H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R370H|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	3037	.	C	T	19713.0	PASS	AF=0.986891;DP=534;DP4=0,0,268,264;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	3290	.	C	G	128.0	min_af_0.050000	AF=0.002266;DP=6620;DP4=5436,1163,11,4;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q1009E|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q191E|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4174	.	TA	T	142.0	min_af_0.050000	AF=0.001279;DP=11728;DP4=9312,2441,11,4;HRUN=5;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K1305|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K1305|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aag/|K487|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	4185	.	G	T	162.0	min_af_0.050000	AF=0.002100;DP=11907;DP4=9344,2535,12,13;SB=31;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G1307V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G489V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4189	.	C	T	93.0	min_af_0.050000	AF=0.001263;DP=11879;DP4=9326,2523,16,3;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1308|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1308|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G490|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G490|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4195	.	T	C	80.0	min_af_0.050000	AF=0.001184;DP=11824;DP4=9348,2459,12,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1310|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T492|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T492|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4308	.	A	G	82.0	min_af_0.050000	AF=0.001455;DP=12371;DP4=2527,9825,6,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1348R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K530R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	4371	.	G	T	90.0	min_af_0.050000	AF=0.001210;DP=13227;DP4=3595,9586,3,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G1369V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G1369V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G551V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G551V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5601	.	T	C	105.0	min_af_0.050000	AF=0.001463;DP=10254;DP4=6843,3393,12,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1779S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1779S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F961S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F961S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5743	.	G	C	1464.0	min_af_0.050000;sb_fdr	AF=0.026248;DP=3124;DP4=1517,1525,11,71;SB=109;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5744	.	T	C	1686.0	min_af_0.050000	AF=0.029789;DP=3122;DP4=1522,1505,19,75;SB=82;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5765	.	G	A	199.0	min_af_0.050000	AF=0.005792;DP=3108;DP4=1726,1363,6,12;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1834S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1016S|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5766	.	G	C	86.0	min_af_0.050000	AF=0.003186;DP=3139;DP4=1768,1358,2,8;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1834A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G1016A|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5812	.	C	T	405.0	min_af_0.050000	AF=0.004460;DP=8745;DP4=1886,6812,12,30;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1849|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1849|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1031|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1031|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	5818	.	TTTAC	T	239.0	min_af_0.050000	AF=0.002052;DP=8773;DP4=1938,6866,3,15;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||cttaca/|LT1853|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1853|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||cttaca/|LT1035|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	6199	.	T	C	116.0	min_af_0.050000	AF=0.001229;DP=26862;DP4=19785,7035,23,11;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1978|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1160|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6242	.	C	T	100.0	min_af_0.050000	AF=0.000795;DP=28921;DP4=20236,8653,20,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1993Y|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H1175Y|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6255	.	C	T	329.0	min_af_0.050000	AF=0.001751;DP=25699;DP4=20282,5363,36,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1997V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1179V|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6297	.	G	A	84.0	min_af_0.050000	AF=0.000761;DP=26296;DP4=19945,6320,17,6;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R2011H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R1193H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6312	.	CA	C	376.0	min_af_0.050000	AF=0.001389;DP=25918;DP4=19826,6183,28,8;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K2017|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K2017|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K1199|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	6352	.	G	C	100.0	min_af_0.050000	AF=0.001539;DP=9749;DP4=4152,5577,7,8;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K2029N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K2029N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K1211N|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaC|K1211N|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6409	.	T	C	110.0	min_af_0.050000	AF=0.000930;DP=23646;DP4=4691,18919,4,20;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2048|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S1230|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6416	.	G	A	95.0	min_af_0.050000	AF=0.000855;DP=23400;DP4=4566,18808,3,19;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V2051I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V2051I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1233I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Ata|V1233I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	6503	.	G	A	133.0	min_af_0.050000	AF=0.001139;DP=20199;DP4=3118,17049,10,19;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A2080T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1262T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	7021	.	TTTA	T	73.0	min_af_0.050000	AF=0.002296;DP=2178;DP4=398,1780,0,5;HRUN=4;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tta/|L2253|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),CODON_DELETION(MODERATE||tta/|L2253|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),CODON_DELETION(MODERATE||tta/|L1435|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),CODON_DELETION(MODERATE||tta/|L1435|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	7889	.	GT	G	353.0	min_af_0.050000	AF=0.005331;DP=4314;DP4=884,3413,6,17;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2543|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2543|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F1725|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	7986	.	A	G	84.0	min_af_0.050000	AF=0.001676;DP=6563;DP4=2932,3615,5,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q2574R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q2574R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1756R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q1756R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	8883	.	T	C	80.0	min_af_0.050000	AF=0.010616;DP=471;DP4=88,377,2,3;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2873T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I2873T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I110T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I110T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	8916	.	T	C	128.0	min_af_0.050000	AF=0.003252;DP=3997;DP4=3121,863,11,2;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2884S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2884S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F121S|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F121S|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	8927	.	GT	G	108.0	min_af_0.050000	AF=0.002195;DP=4100;DP4=3161,931,6,3;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F2889|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F2889|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F126|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	9014	.	G	A	85.0	min_af_0.050000	AF=0.002464;DP=4058;DP4=3162,885,7,3;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2917T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A154T|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	9016	.	T	C	93.0	min_af_0.050000	AF=0.002467;DP=4054;DP4=3162,882,8,2;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2917|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A2917|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A154|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A154|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	9208	.	T	C	84.0	min_af_0.050000	AF=0.002427;DP=3708;DP4=685,3012,3,7;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2981|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S2981|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S218|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S218|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	9600	.	T	C	90.0	min_af_0.050000	AF=0.001700;DP=8237;DP4=6499,1722,10,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L3112S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L3112S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L349S|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L349S|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	10046	.	GTTT	G	72.0	min_af_0.050000	AF=0.006144;DP=651;DP4=152,496,1,3;HRUN=4;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL3261V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL3261V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL498V|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttg/gtg|VL498V|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2	10386	.	CT	C	99.0	min_af_0.050000	AF=0.002298;DP=3481;DP4=2009,1466,4,4;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S3376|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S3376|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S113|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S113|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	11036	.	CTTTTAG	C	127.0	min_af_0.050000	AF=0.001090;DP=11931;DP4=10092,1826,12,1;HRUN=4;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV3593V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV3593V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV24V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gttttagtc/gtc|VLV24V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2	11067	.	C	T	159.0	min_af_0.050000	AF=0.001731;DP=12712;DP4=10344,2335,18,10;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S3601F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S3601F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S32F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S32F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11071	.	G	GTTC	49314.0	PASS	AF=0.919205;DP=12736;DP4=800,227,9565,2142;HRUN=2;SB=24;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F3604FF|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|GTTC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTTt|F35FF|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|GTTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2	11074	.	C	CTTCT	3762.0	min_af_0.050000	AF=0.026300;DP=13004;DP4=10107,2533,282,60;HRUN=8;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F3604FF?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CTTCT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTTTt|F35FF?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|CTTCT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	11075	.	T	TTC	7808.0	min_af_0.050000	AF=0.025871;DP=13026;DP4=10138,2548,273,64;HRUN=8;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F3604F?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTC|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/ttCTt|F35F?|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	11075	.	T	TTCC	208.0	min_af_0.050000	AF=0.001382;DP=13026;DP4=10138,2548,15,3;HRUN=8;SB=0;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F3604FL|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TTCC|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCCTt|F35FL|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TTCC|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2	11076	.	T	TCTC	120.0	min_af_0.050000	AF=0.000915;DP=13115;DP4=10415,2686,8,4;HRUN=8;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F3604FS|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|TCTC),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F3604FS|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|TCTC),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F35FS|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|TCTC|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||ttt/ttCTCt|F35FS|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|TCTC|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11077	.	T	C	217.0	min_af_0.050000	AF=0.008991;DP=13124;DP4=10364,2639,66,55;SB=90;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F3604|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F35|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11083	.	G	T	86.0	min_af_0.050000	AF=0.003262;DP=13183;DP4=10380,2749,31,18;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L3606F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L37F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11104	.	T	C	126.0	min_af_0.050000	AF=0.001408;DP=13493;DP4=10490,2969,16,6;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P3613|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P44|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11139	.	C	T	123.0	min_af_0.050000	AF=0.001387;DP=13695;DP4=10485,3180,15,11;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3625V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A56V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11442	.	C	T	1697.0	min_af_0.050000	AF=0.020029;DP=4893;DP4=3611,1179,71,28;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3726V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3726V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A157V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A157V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11653	.	CT	C	106.0	min_af_0.050000	AF=0.001023;DP=10755;DP4=6029,4718,5,6;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C3798|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C3798|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C229|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	11851	.	G	A	153.0	min_af_0.050000	AF=0.002485;DP=6840;DP4=1562,5257,2,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3862I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3862I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3I|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M3I|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	11866	.	C	T	107.0	min_af_0.050000	AF=0.001932;DP=7247;DP4=1487,5740,4,12;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3867|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C3867|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C8|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C8|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12129	.	C	T	81.0	min_af_0.050000	AF=0.001191;DP=10917;DP4=2183,8720,2,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A3955V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A13V|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12132	.	CTT	C	80.0	min_af_0.050000	AF=0.000827;DP=10886;DP4=2133,8761,1,8;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F3957|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F3957|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F15|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F15|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2	12143	.	G	A	100.0	min_af_0.050000	AF=0.001349;DP=11858;DP4=3081,8755,3,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A3960T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A18T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12662	.	G	A	100.0	min_af_0.050000	AF=0.001730;DP=8093;DP4=1723,6352,3,11;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12684	.	A	G	217.0	min_af_0.050000	AF=0.002858;DP=8048;DP4=1686,6335,8,18;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4140R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION(MODERATE|MISSENSE|cAg/cGg|Q198R|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	12769	.	G	A	80.0	min_af_0.050000	AF=0.001019;DP=18646;DP4=10427,8187,11,9;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4168|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A4168|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A28|112|ORF1ab|protein_coding|CODING|YP_009725305.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A28|112|ORF1ab|protein_coding|CODING|YP_009742616.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13034	.	G	A	131.0	min_af_0.050000	AF=0.000871;DP=32142;DP4=19137,12963,17,16;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4257T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13035	.	C	T	140.0	min_af_0.050000	AF=0.000899;DP=32264;DP4=19148,13078,18,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4257V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4257V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13038	.	C	T	94.0	min_af_0.050000	AF=0.000712;DP=32326;DP4=19147,13141,13,12;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4258I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T4258I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5I|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5I|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13048	.	T	C	93.0	min_af_0.050000	AF=0.000709;DP=32455;DP4=19069,13247,19,99;SB=209;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4261|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P8|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13049	.	G	A	90.0	min_af_0.050000	AF=0.000707;DP=32554;DP4=19096,13425,19,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4262T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A9T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13051	.	C	T	49314.0	PASS	AF=0.968256;DP=32510;DP4=506,283,18579,13137;SB=27;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A4262|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A4262|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A9|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A9|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13078	.	T	C	104.0	min_af_0.050000	AF=0.000897;DP=23404;DP4=18810,4560,17,5;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A4271|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A18|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13094	.	G	A	105.0	min_af_0.050000	AF=0.001062;DP=23533;DP4=18300,5201,17,9;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A4277T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A24T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13123	.	TG	T	121.0	min_af_0.050000	AF=0.000734;DP=23172;DP4=17672,5522,15,2;HRUN=5;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||gga/|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gga/|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11)
NC_045512.2	13129	.	A	G	245.0	min_af_0.050000	AF=0.001754;DP=23381;DP4=17726,5589,47,13;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G4288|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G35|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13142	.	AATT	A	92.0	min_af_0.050000	AF=0.000522;DP=22996;DP4=17663,5362,11,1;HRUN=2;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC4293S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattgt/agt|NC40S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13182	.	A	G	82.0	min_af_0.050000	AF=0.001402;DP=9270;DP4=4206,5046,7,9;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4306R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q4306R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q53R|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q53R|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13235	.	G	A	121.0	min_af_0.050000	AF=0.001286;DP=21767;DP4=5218,16517,5,24;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4324T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A71T|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13240	.	G	A	81.0	min_af_0.050000	AF=0.000912;DP=21941;DP4=5298,16616,7,15;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S4325|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S72|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13267	.	A	G	88.0	min_af_0.050000	AF=0.000835;DP=22744;DP4=5283,17428,7,13;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I4334M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I4334M|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I81M|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I81M|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13288	.	AT	A	105.0	min_af_0.050000	AF=0.000617;DP=22682;DP4=5257,17413,2,12;HRUN=4;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C4343|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C4343|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgt/|C90|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11)
NC_045512.2	13299	.	TA	T	84.0	min_af_0.050000	AF=0.000537;DP=22351;DP4=5178,17249,3,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K4346|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K4346|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K93|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.11)
NC_045512.2	13345	.	T	C	90.0	min_af_0.050000	AF=0.000911;DP=25238;DP4=8015,17183,13,14;SB=10;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P4360|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P107|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13385	.	G	A	118.0	min_af_0.050000	AF=0.002796;DP=6437;DP4=5404,1009,16,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G4374S|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G121S|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13451	.	G	A	128.0	min_af_0.050000	AF=0.002564;DP=5850;DP4=4711,1123,9,6;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4396T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|12|ORF1ab|protein_coding|CODING|YP_009725312.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13571	.	G	T	198.0	min_af_0.050000	AF=0.003149;DP=6351;DP4=1257,5071,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G4436V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G44V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13586	.	TA	T	78.0	min_af_0.050000	AF=0.001270;DP=6299;DP4=1240,5075,2,6;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||act/|T4443|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||act/|T51|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	13726	.	GTT	G	148.0	min_af_0.050000	AF=0.000684;DP=24841;DP4=19872,5001,14,3;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V4488|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),FRAME_SHIFT(HIGH||gtt/|V96|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	13860	.	C	T	87.0	min_af_0.050000	AF=0.000792;DP=25262;DP4=5217,20021,3,19;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D4532|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D140|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13924	.	TG	T	102.0	min_af_0.050000	AF=0.000538;DP=24171;DP4=4056,20138,6,7;HRUN=2;SB=18;INDEL;EFF=FRAME_SHIFT(HIGH||tgg/|W4554|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tgg/|W162|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	13966	.	G	A	112.0	min_af_0.050000	AF=0.001448;DP=13119;DP4=11254,1837,19,4;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4568T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A176T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	13982	.	G	A	568.0	min_af_0.050000	AF=0.004640;DP=11637;DP4=9528,2049,31,23;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R4573H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cAt|R181H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14000	.	T	C	109.0	min_af_0.050000	AF=0.001423;DP=11244;DP4=8939,2280,12,9;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L4579S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L187S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14029	.	C	T	86.0	min_af_0.050000	AF=0.001223;DP=11445;DP4=8903,2521,14,3;SB=0;EFF=STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R4589*|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R197*|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14197	.	G	A	132.0	min_af_0.050000	AF=0.001690;DP=10653;DP4=2082,8545,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A4645T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A253T|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14199	.	A	G	92.0	min_af_0.050000	AF=0.001321;DP=10596;DP4=2048,8528,3,14;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A4645|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A253|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14408	.	C	T	38664.0	PASS	AF=0.993204;DP=1030;DP4=0,0,481,548;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14615	.	G	A	104.0	min_af_0.050000	AF=0.001821;DP=8237;DP4=6659,1562,14,1;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R4784H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R392H|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14625	.	CT	C	77.0	min_af_0.050000	AF=0.000960;DP=8333;DP4=6724,1619,4,4;HRUN=4;SB=12;INDEL;EFF=FRAME_SHIFT(HIGH||tca/|S4789|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tca/|S397|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	14779	.	A	G	83.0	min_af_0.050000	AF=0.001441;DP=8325;DP4=1551,6758,1,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N4839D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N447D|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	14848	.	CTATTTG	C	146.0	min_af_0.050000	AF=0.001520;DP=7894;DP4=1373,6562,1,11;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tttgta/|FV4863|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),CODON_DELETION(MODERATE||tttgta/|FV471|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2	14852	.	TTG	T	101.0	min_af_0.050000	AF=0.001143;DP=7873;DP4=1346,6528,2,7;HRUN=3;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gta/|V4864|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gta/|V472|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	14877	.	C	T	99.0	min_af_0.050000	AF=0.001715;DP=7580;DP4=1121,6438,1,18;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y4871|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y479|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15324	.	C	T	49314.0	PASS	AF=0.987428;DP=4852;DP4=1,0,3671,1180;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N5020|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N628|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15557	.	C	T	97.0	min_af_0.050000	AF=0.001120;DP=15182;DP4=12030,3125,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5098V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A706V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15587	.	C	T	125.0	min_af_0.050000	AF=0.001359;DP=15452;DP4=11989,3428,16,8;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A5108V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A716V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15599	.	T	C	133.0	min_af_0.050000	AF=0.001423;DP=15462;DP4=11902,3523,20,10;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V5112A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V720A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15673	.	T	G	154.0	min_af_0.050000;sb_fdr	AF=0.004353;DP=5743;DP4=2619,3096,22,3;SB=47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F5137V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Gtt|F745V|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15682	.	T	A	2513.0	min_af_0.050000	AF=0.025192;DP=5716;DP4=2676,2893,80,66;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y5140N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tat/Aat|Y748N|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15685	.	T	A	2366.0	min_af_0.050000	AF=0.024344;DP=5751;DP4=2707,2901,79,63;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L5141M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Atg|L749M|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15761	.	G	C	128.0	min_af_0.050000	AF=0.001343;DP=14896;DP4=3157,11712,5,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G5166A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G774A|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15784	.	T	TGAC	101.0	min_af_0.050000	AF=0.000738;DP=14904;DP4=3226,11771,4,7;HRUN=3;SB=5;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F5174*L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|TGAC),STOP_GAINED+CODON_CHANGE_PLUS_CODON_INSERTION(HIGH||ttt/tGACtt|F782*L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|TGAC|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15788	.	AGTC	A	102.0	min_af_0.050000	AF=0.000744;DP=14787;DP4=3096,11695,4,7;HRUN=1;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS5175K|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aagtca/aaa|KS783K|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15814	.	GT	G	83.0	min_af_0.050000	AF=0.000757;DP=14525;DP4=2939,11605,0,11;HRUN=5;SB=8;INDEL;EFF=FRAME_SHIFT(HIGH||ttt/|F5185|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ttt/|F793|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	15848	.	CTG	C	87.0	min_af_0.050000	AF=0.000656;DP=15239;DP4=2208,13051,3,7;HRUN=1;SB=7;INDEL;EFF=FRAME_SHIFT(HIGH||actgac/|TD5195|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||actgac/|TD803|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	15870	.	T	C	85.0	min_af_0.050000	AF=0.001034;DP=14505;DP4=12263,2225,11,4;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5202|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H810|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15878	.	G	A	117.0	min_af_0.050000	AF=0.001285;DP=14781;DP4=12233,2469,71,2;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C5205Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C813Y|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15905	.	A	G	94.0	min_af_0.050000	AF=0.001148;DP=13939;DP4=10972,2946,14,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q5214R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q822R|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	15961	.	G	A	87.0	min_af_0.050000	AF=0.001195;DP=14228;DP4=11028,3178,13,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G5233S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G841S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	16072	.	G	T	109.0	min_af_0.050000	AF=0.001374;DP=13827;DP4=2871,10926,3,20;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A5270S|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A878S|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	16110	.	G	A	114.0	min_af_0.050000	AF=0.001321;DP=13630;DP4=2821,10780,7,13;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K5282|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K890|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	16127	.	C	T	89.0	min_af_0.050000	AF=0.001127;DP=13309;DP4=2569,10720,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T5288I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T896I|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	16837	.	GA	G	159.0	min_af_0.050000	AF=0.002455;DP=5295;DP4=4078,1223,11,2;HRUN=5;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K5526|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K202|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	17104	.	C	T	125.0	min_af_0.050000	AF=0.001531;DP=11760;DP4=6999,4735,10,11;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H5614Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H290Y|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	17183	.	C	T	80.0	min_af_0.050000	AF=0.001379;DP=8701;DP4=6683,2003,8,4;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5640V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A316V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	17339	.	C	T	84.0	min_af_0.050000	AF=0.001407;DP=9239;DP4=2216,7005,2,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A5692V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A368V|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18669	.	T	C	84.0	min_af_0.050000	AF=0.001497;DP=8014;DP4=6457,1536,13,0;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C6135|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C210|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18687	.	CT	C	119.0	min_af_0.050000	AF=0.001340;DP=8210;DP4=6530,1683,10,1;HRUN=4;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||tcc/|S6143|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||tcc/|S218|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	18715	.	T	C	91.0	min_af_0.050000	AF=0.001573;DP=8263;DP4=6484,1760,12,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C6151R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C226R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18718	.	T	C	93.0	min_af_0.050000	AF=0.001566;DP=8302;DP4=6496,1793,10,3;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W6152R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W227R|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18932	.	T	C	80.0	min_af_0.050000	AF=0.000882;DP=18140;DP4=10385,7693,13,45;SB=71;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I6223T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I298T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	18998	.	C	T	102.0	min_af_0.050000	AF=0.001323;DP=12090;DP4=9600,2461,16,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6245V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A320V|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19029	.	C	T	81.0	min_af_0.050000	AF=0.001222;DP=12278;DP4=9707,2551,16,1;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H6255|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H330|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19199	.	G	A	82.0	min_af_0.050000	AF=0.001118;DP=12520;DP4=2574,9929,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C6312Y|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C387Y|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19219	.	G	A	85.0	min_af_0.050000	AF=0.001153;DP=12139;DP4=2262,9858,5,13;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A6319T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A394T|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19611	.	A	G	103.0	min_af_0.050000	AF=0.001440;DP=11113;DP4=8992,2101,12,5;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T6449|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T524|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19679	.	G	T	113.0	min_af_0.050000	AF=0.001523;DP=11821;DP4=9213,2586,16,2;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G6472V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G20V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19801	.	C	T	88.0	min_af_0.050000	AF=0.001376;DP=10904;DP4=2116,8770,3,13;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R6513C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R61C|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19814	.	CAG	C	239.0	min_af_0.050000	AF=0.001755;DP=10824;DP4=2128,8719,4,15;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||ccagta/|PV6517|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),FRAME_SHIFT(HIGH||ccagta/|PV65|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON);LOF=(ORF1ab|GU280_gp01|28|0.07)
NC_045512.2	19870	.	G	A	153.0	min_af_0.050000	AF=0.001802;DP=11100;DP4=2451,8624,3,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V6536M|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V84M|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	19970	.	C	T	98.0	min_af_0.050000	AF=0.007973;DP=878;DP4=657,214,4,3;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A6569V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A117V|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	20937	.	G	A	108.0	min_af_0.050000	AF=0.001625;DP=10463;DP4=8160,2282,17,3;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T6891|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T93|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	21054	.	C	T	124.0	min_af_0.050000	AF=0.001835;DP=9808;DP4=1973,7804,4,16;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y6930|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y132|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2	21073	.	GT	G	66.0	min_af_0.050000	AF=0.000733;DP=9549;DP4=1843,7727,2,5;HRUN=2;SB=2;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V6937|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||gtt/|V139|297|ORF1ab|protein_coding|CODING|YP_009725311.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.04)
NC_045512.2	22218	.	GT	G	147.0	min_af_0.050000	AF=0.004186;DP=2389;DP4=435,1949,2,8;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||tcg/|S221|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2	22643	.	T	A	801.0	min_af_0.050000	AF=0.005735;DP=11508;DP4=9198,2236,51,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Agt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2	22644	.	G	C	746.0	min_af_0.050000	AF=0.005540;DP=11553;DP4=9197,2280,47,17;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tCt|C361S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	22645	.	T	A	749.0	min_af_0.050000	AF=0.005544;DP=11543;DP4=9171,2285,52,16;SB=3;EFF=STOP_GAINED(HIGH|NONSENSE|tgT/tgA|C361*|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2	22859	.	G	C	117.0	min_af_0.050000	AF=0.001528;DP=11125;DP4=2468,8618,7,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V433L|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	23132	.	GT	G	179.0	min_af_0.050000	AF=0.003890;DP=2828;DP4=462,2364,0,11;HRUN=3;SB=6;INDEL;EFF=FRAME_SHIFT(HIGH||tgt/|C525|1273|S|protein_coding|CODING|GU280_gp02|1|G|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512.2	23163	.	T	C	117.0	min_af_0.050000	AF=0.001396;DP=12895;DP4=9870,2998,17,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V534A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	23272	.	T	C	154.0	min_af_0.050000	AF=0.001679;DP=13105;DP4=9931,3147,18,6;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A570|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	23403	.	A	G	49314.0	PASS	AF=0.990102;DP=12730;DP4=3,3,2828,9889;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2	23438	.	G	A	93.0	min_af_0.050000	AF=0.001224;DP=12256;DP4=2589,9647,4,12;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A626T|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2	23439	.	C	T	145.0	min_af_0.050000	AF=0.001639;DP=12203;DP4=2550,9627,7,15;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A626V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2	23781	.	T	C	92.0	min_af_0.050000	AF=0.003842;DP=2082;DP4=391,1681,2,7;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	24729	.	C	T	143.0	min_af_0.050000	AF=0.001381;DP=15926;DP4=13029,2871,17,7;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A1056V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2	24780	.	A	G	180.0	min_af_0.050000	AF=0.001600;DP=16878;DP4=13508,3337,21,7;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K1073R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2	24794	.	G	A	88.0	min_af_0.050000	AF=0.000996;DP=17063;DP4=13392,3645,14,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1078T|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2	24799	.	T	C	199.0	min_af_0.050000	AF=0.001639;DP=17083;DP4=13407,3641,25,8;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1079|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	24942	.	A	T	607.0	min_af_0.050000	AF=0.003550;DP=16901;DP4=3607,13223,3,62;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D1127V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2	24952	.	AGGAATT	A	84.0	min_af_0.050000	AF=0.000594;DP=16836;DP4=3631,13204,1,9;HRUN=2;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggaattgtc/gtc|GIV1131V|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2	24972	.	T	C	153.0	min_af_0.050000	AF=0.001433;DP=16743;DP4=3598,13107,6,22;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V1137A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2	24986	.	C	T	112.0	min_af_0.050000	AF=0.001156;DP=16431;DP4=3383,13022,5,14;SB=2;EFF=STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q1142*|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2	25320	.	G	A	85.0	min_af_0.050000	AF=0.001360;DP=9562;DP4=7908,1633,14,1;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C1253Y|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2	25543	.	G	A	139.0	min_af_0.050000	AF=0.001802;DP=10546;DP4=2037,8488,5,14;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A51T|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2	25587	.	CA	C	124.0	min_af_0.050000	AF=0.001269;DP=10247;DP4=1857,8407,2,11;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K67|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00)
NC_045512.2	25618	.	G	A	83.0	min_af_0.050000	AF=0.001432;DP=9779;DP4=1482,8279,5,12;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G76S|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2	25936	.	C	T	174.0	min_af_0.050000	AF=0.002066;DP=10167;DP4=8332,1810,19,3;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H182Y|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2	25982	.	TA	T	80.0	min_af_0.050000	AF=0.000829;DP=10857;DP4=8636,2216,7,2;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K198|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T|INFO_REALIGN_3_PRIME);LOF=(ORF3a|GU280_gp03|1|1.00)
NC_045512.2	26042	.	C	T	1909.0	min_af_0.050000	AF=0.011118;DP=11693;DP4=8824,2733,98,34;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T217I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2	26044	.	C	G	1780.0	min_af_0.050000	AF=0.010469;DP=11653;DP4=8800,2722,94,32;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q218E|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G)
NC_045512.2	26046	.	A	G	1835.0	min_af_0.050000	AF=0.010734;DP=11738;DP4=8835,2772,96,33;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q218|275|ORF3a|protein_coding|CODING|GU280_gp03|1|G)
NC_045512.2	26057	.	A	C	80.0	min_af_0.050000	AF=0.002228;DP=6734;DP4=3992,2718,9,9;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D222A|275|ORF3a|protein_coding|CODING|GU280_gp03|1|C)
NC_045512.2	26089	.	T	A	108.0	min_af_0.050000	AF=0.002580;DP=4652;DP4=2165,2473,2,11;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Aac|Y233N|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2	26103	.	T	A	659.0	min_af_0.050000;sb_fdr	AF=0.009765;DP=4813;DP4=2371,2394,43,4;SB=86;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V237|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2	26141	.	A	T	87.0	min_af_0.050000	AF=0.002355;DP=4670;DP4=2711,1943,2,9;SB=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gTc|D250V|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2	26209	.	G	A	178.0	min_af_0.050000	AF=0.001966;DP=11696;DP4=2612,9054,8,18;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V273M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|A)
NC_045512.2	26542	.	C	A	184.0	min_af_0.050000	AF=0.006467;DP=2165;DP4=107,2043,0,14;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T7N|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2	26545	.	T	G	296.0	min_af_0.050000	AF=0.002439;DP=15173;DP4=13033,2102,24,13;SB=30;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTt/aGt|I8S|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2	26561	.	TA	T	220.0	min_af_0.050000	AF=0.001461;DP=15742;DP4=13196,2525,18,5;HRUN=5;SB=3;INDEL;EFF=FRAME_SHIFT(HIGH||aag/|K15|222|M|protein_coding|CODING|GU280_gp05|1|T|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	26774	.	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	96.0	min_af_0.050000	AF=0.000650;DP=16926;DP4=3341,13613,1,10;HRUN=2;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/|ACLVGLMWLSYFIASFRLF85|222|M|protein_coding|CODING|GU280_gp05|1|G);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	26775	.	GCTTGT	G	95.0	min_af_0.050000	AF=0.000653;DP=16845;DP4=3334,13588,2,9;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||cttgta/|LV87|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	26775	.	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	134.0	min_af_0.050000	AF=0.000831;DP=16845;DP4=3334,13588,1,13;HRUN=1;SB=4;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc|CLVGLMWLSYFIASF86F|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2	26779	.	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	121.0	min_af_0.050000	AF=0.000769;DP=16910;DP4=3320,13623,0,13;HRUN=1;SB=10;INDEL;EFF=FRAME_SHIFT(HIGH||gtaggcttgatgtggctcagctacttcattgcttctttc/|VGLMWLSYFIASF88|222|M|protein_coding|CODING|GU280_gp05|1|G|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	26786	.	AGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	A	161.0	min_af_0.050000	AF=0.000947;DP=16887;DP4=3297,13606,1,15;HRUN=2;SB=4;INDEL;EFF=FRAME_SHIFT(HIGH||ggcttgatgtggctcagctacttcattgcttctttc/|GLMWLSYFIASF89|222|M|protein_coding|CODING|GU280_gp05|1|A);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	26788	.	G	A	136.0	min_af_0.050000	AF=0.001295;DP=16992;DP4=3364,13533,3,20;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G89D|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2	26814	.	G	A	83.0	min_af_0.050000	AF=0.000954;DP=16775;DP4=3241,13438,2,16;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A98T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2	26847	.	A	G	80.0	min_af_0.050000	AF=0.001002;DP=16958;DP4=2751,14184,4,15;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M109V|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2	26873	.	C	T	238.0	min_af_0.050000	AF=0.001445;DP=24907;DP4=10532,14329,20,17;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N117|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2	26889	.	C	T	169.0	min_af_0.050000	AF=0.001294;DP=24736;DP4=10265,14432,18,17;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P123S|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2	27093	.	T	C	87.0	min_af_0.050000	AF=0.001158;DP=12956;DP4=3003,9931,3,12;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S191P|222|M|protein_coding|CODING|GU280_gp05|1|C)
NC_045512.2	27103	.	C	T	84.0	min_af_0.050000	AF=0.001153;DP=13015;DP4=3020,9979,4,11;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A194V|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512.2	27105	.	G	A	184.0	min_af_0.050000	AF=0.001854;DP=12942;DP4=3010,9897,7,19;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A195T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2	27133	.	ATAAATT	A	82.0	min_af_0.050000	AF=0.000704;DP=12790;DP4=2878,9896,2,7;HRUN=1;SB=0;INDEL;EFF=STOP_GAINED+CODON_CHANGE_PLUS_CODON_DELETION(HIGH||tataaatta/taa|YKL204*|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2	27133	.	ATAAAT	A	122.0	min_af_0.050000	AF=0.000938;DP=12790;DP4=2878,9896,2,10;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ttaaac/|LN206|222|M|protein_coding|CODING|GU280_gp05|1|A|INFO_REALIGN_3_PRIME);LOF=(M|GU280_gp05|1|1.00)
NC_045512.2	27190	.	AAGTGACAACAGATGTTTCATCTCGTTGACTT	A	84.0	min_af_0.050000	AF=0.000862;DP=12759;DP4=10963,11010,10,1;HRUN=2;SB=22;INDEL;EFF=GENE_FUSION(HIGH|||||M+ORF6||CODING|||A),FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION(HIGH||taa/|*223|222|M|protein_coding|CODING|GU280_gp05|1|A),FRAME_SHIFT+START_LOST(HIGH||atgtttcatctcgttgacttt/|MFHLVDF1|61|ORF6|protein_coding|CODING|GU280_gp06|1|A);LOF=(ORF6|GU280_gp06|1|1.00)
NC_045512.2	27282	.	G	A	92.0	min_af_0.050000	AF=0.001215;DP=12350;DP4=9873,2456,13,6;SB=6;EFF=STOP_GAINED(HIGH|NONSENSE|tgG/tgA|W27*|61|ORF6|protein_coding|CODING|GU280_gp06|1|A)
NC_045512.2	27285	.	T	A	188.0	min_af_0.050000	AF=0.001946;DP=12333;DP4=9873,2431,23,1;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N28K|61|ORF6|protein_coding|CODING|GU280_gp06|1|A)
NC_045512.2	27335	.	C	T	427.0	min_af_0.050000	AF=0.007644;DP=4317;DP4=2285,1996,22,12;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T45I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512.2	27344	.	A	T	816.0	min_af_0.050000	AF=0.012494;DP=4322;DP4=2322,1944,35,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K48I|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512.2	27345	.	A	T	813.0	min_af_0.050000	AF=0.012500;DP=4320;DP4=2323,1943,35,19;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K48N|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512.2	27354	.	A	G	859.0	min_af_0.050000	AF=0.013456;DP=4236;DP4=2370,1805,45,14;SB=24;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q51|61|ORF6|protein_coding|CODING|GU280_gp06|1|G)
NC_045512.2	27416	.	C	T	90.0	min_af_0.050000	AF=0.001178;DP=12734;DP4=2572,10143,2,13;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A8V|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512.2	27437	.	G	A	143.0	min_af_0.050000	AF=0.001595;DP=12541;DP4=2423,10091,2,19;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C15Y|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
NC_045512.2	27496	.	T	C	98.0	min_af_0.050000	AF=0.001317;DP=11388;DP4=1594,9778,3,12;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C35R|121|ORF7a|protein_coding|CODING|GU280_gp07|1|C)
NC_045512.2	28138	.	C	T	99.0	min_af_0.050000	AF=0.001215;DP=13167;DP4=11097,2039,13,5;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S82F|121|ORF8|protein_coding|CODING|GU280_gp09|1|T)
NC_045512.2	28148	.	T	C	83.0	min_af_0.050000	AF=0.001078;DP=12985;DP4=11170,1792,13,1;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P85|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2	28342	.	A	G	112.0	min_af_0.050000	AF=0.001261;DP=14272;DP4=2718,11531,4,15;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S23|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2	28378	.	G	A	103.0	min_af_0.050000	AF=0.001371;DP=13857;DP4=2379,11440,1,18;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A35|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	28378	.	G	C	86.0	min_af_0.050000	AF=0.001227;DP=13857;DP4=2379,11440,5,12;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A35|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2	28380	.	G	A	241.0	min_af_0.050000	AF=0.002170;DP=13827;DP4=2341,11452,10,21;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R36Q|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	28383	.	CA	C	82.0	min_af_0.050000	AF=0.000728;DP=13736;DP4=2329,11456,1,9;HRUN=4;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||aaa/|K38|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2	28774	.	G	A	80.0	min_af_0.050000	AF=0.001870;DP=5348;DP4=4300,1036,9,1;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L167|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	28953	.	T	C	88.0	min_af_0.050000	AF=0.002090;DP=5264;DP4=1078,4174,3,8;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L227S|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2	28987	.	CCAA	C	391.0	min_af_0.050000	AF=0.004456;DP=5611;DP4=983,4617,8,17;HRUN=2;SB=11;INDEL;EFF=CODON_DELETION(MODERATE||caa/|Q242|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2	29029	.	T	C	858.0	min_af_0.050000	AF=0.004277;DP=18704;DP4=12752,5860,51,36;SB=13;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A252|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2	29039	.	A	T	1871.0	min_af_0.050000	AF=0.007569;DP=19026;DP4=12781,6088,89,57;SB=10;EFF=STOP_GAINED(HIGH|NONSENSE|Aag/Tag|K256*|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2	29049	.	G	A	326.0	min_af_0.050000	AF=0.002664;DP=15392;DP4=12862,2473,41,5;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R259Q|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	29081	.	GTA	G	75.0	min_af_0.050000	AF=0.000573;DP=15701;DP4=12808,2895,8,1;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||gta/|V270|419|N|protein_coding|CODING|GU280_gp10|1|G);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2	29098	.	C	T	97.0	min_af_0.050000	AF=0.001203;DP=15799;DP4=12816,2957,16,3;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G275|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2	29132	.	G	A	85.0	min_af_0.050000	AF=0.001063;DP=15987;DP4=12972,2987,17,5;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G287R|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2	29187	.	C	T	143.0	min_af_0.050000	AF=0.002863;DP=5589;DP4=3055,2517,10,6;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A305V|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2	29188	.	A	G	96.0	min_af_0.050000	AF=0.002168;DP=5536;DP4=3042,2470,8,9;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A305|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512.2	29195	.	GC	G	173.0	min_af_0.050000	AF=0.002574;DP=5439;DP4=3065,2377,8,6;HRUN=5;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||ccc/|P309|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME);LOF=(N|GU280_gp10|1|1.00)
NC_045512.2	29259	.	C	T	80.0	min_af_0.050000	AF=0.001072;DP=15862;DP4=2960,12882,4,14;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T329M|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2	29322	.	T	C	86.0	min_af_0.050000	AF=0.001005;DP=15925;DP4=3242,12646,5,18;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V350A|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2	29348	.	G	A	112.0	min_af_0.050000	AF=0.001238;DP=15350;DP4=2783,12536,2,21;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A359T|419|N|protein_coding|CODING|GU280_gp10|1|A)