# HG changeset patch
# User iuc
# Date 1592511109 14400
# Node ID 2a3a00c1fa0a12421dad2f310ff7bf844ffa1ff0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"
diff -r 000000000000 -r 2a3a00c1fa0a snpEff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff.xml Thu Jun 18 16:11:49 2020 -0400
@@ -0,0 +1,363 @@
+
+ annotate variants for SARS-CoV-2
+
+ snpEff_macros.xml
+
+
+
+
+
+
+ '$snpeff_output'
+
+ #if $statsFile:
+ &&
+ #import os
+ #if $csvStats:
+ #set $genes_file = str($csvFile) + '.genes.txt'
+ #else
+ #set $genes_file = str($statsFile) + '.genes.txt'
+ #end if
+ #set $genes_file_name = os.path.split($genes_file)[-1]
+ mkdir '$statsFile.files_path' &&
+ mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
+ #end if
+ #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
+ &&
+ ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
+ sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
+ #end if
+ ]]>
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+ By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
+ You can prepend any string you want to the chromosome name
+
+ ^\S*$
+
+
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+ generate_stats == True
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+ csvStats == True
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diff -r 000000000000 -r 2a3a00c1fa0a snpEff_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_macros.xml Thu Jun 18 16:11:49 2020 -0400
@@ -0,0 +1,51 @@
+
+
+ snpeff
+
+
+
+
+
+
+
+
+
+
+
+ 4.5covid19
+ SnpEff4.5
+ -Xmx\${GALAXY_MEMORY_MB:-8192}m
+
+
+
+-------
+
+To learn more about SnpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
+
+
+
+-------
+
+.. class:: warningmark
+
+**Databases in the SnpEff Covid-19 edition**
+
+This special version of SnpEff provides only a fixed number of
+SARS-CoV-2-related genome databases.
+
+Unlike with regular SnpEff releases, it is not possible to extend this set,
+*i.e*, you cannot download additional databases or build custom databases for
+this edition.
+
+
+
+
+
+
+ 10.4161/fly.19695
+
+
+
+
diff -r 000000000000 -r 2a3a00c1fa0a test-data/input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf Thu Jun 18 16:11:49 2020 -0400
@@ -0,0 +1,103 @@
+##fileformat=VCFv4.0
+##fileDate=20200606
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/008/613/8613450/working/pp-tmp/lofreq2_call_paralleltqdqbfki/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER= 0.001000">
+##FILTER=
+##FILTER=
+#CHROM POS ID REF ALT QUAL FILTER INFO
+NC_045512.2 105 . G T 3155.0 PASS DP=748;AF=0.171123;SB=0;DP4=600,20,124,4
+NC_045512.2 443 . GT G 99.0 PASS DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4
+NC_045512.2 507 . ATGGTCATGTTATGGT A 100.0 PASS DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1
+NC_045512.2 509 . GGTCATGTTATGGTT G 99.0 PASS DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2
+NC_045512.2 514 . TGTTATG T 118.0 PASS DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1
+NC_045512.2 515 . GTTATGGTT G 59.0 PASS DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2
+NC_045512.2 517 . TATG T 91.0 PASS DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1
+NC_045512.2 518 . ATG A 53.0 PASS DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1
+NC_045512.2 518 . ATGGTT A 78.0 PASS DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1
+NC_045512.2 685 . AAAGTCATTT A 60.0 PASS DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3
+NC_045512.2 1011 . ATG A 77.0 PASS DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1
+NC_045512.2 1135 . G GA 93.0 PASS DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5
+NC_045512.2 1349 . C CA 257.0 PASS DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4
+NC_045512.2 1730 . G A 116.0 PASS DP=997;AF=0.009027;SB=2;DP4=440,548,5,4
+NC_045512.2 1946 . G GT 206.0 PASS DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4
+NC_045512.2 2185 . G GT 73.0 PASS DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3
+NC_045512.2 2310 . TA T 56.0 PASS DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3
+NC_045512.2 2480 . A G 49314.0 PASS DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196
+NC_045512.2 2558 . C T 49314.0 PASS DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402
+NC_045512.2 2612 . G GT 58.0 PASS DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3
+NC_045512.2 3259 . G T 69.0 PASS DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0
+NC_045512.2 3412 . T TA 69.0 PASS DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5
+NC_045512.2 3448 . C CA 59.0 PASS DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2
+NC_045512.2 3545 . AATG A 57.0 PASS DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2
+NC_045512.2 4148 . G GT 63.0 PASS DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4
+NC_045512.2 6287 . TG T 60.0 PASS DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2
+NC_045512.2 6696 . C CT 1002.0 PASS DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4
+NC_045512.2 6696 . C T 141.0 PASS DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10
+NC_045512.2 7504 . C CA 57.0 PASS DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3
+NC_045512.2 9118 . C T 170.0 PASS DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11
+NC_045512.2 9502 . C T 221.0 PASS DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12
+NC_045512.2 9701 . AT A 59.0 PASS DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3
+NC_045512.2 10605 . C CT 116.0 PASS DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4
+NC_045512.2 10619 . C A 235.0 PASS DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13
+NC_045512.2 10660 . TA T 122.0 PASS DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2
+NC_045512.2 11074 . C CT 281.0 PASS DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8
+NC_045512.2 11082 . TG T 1843.0 PASS DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1
+NC_045512.2 11083 . G T 39536.0 PASS DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595
+NC_045512.2 11133 . CT C 60.0 PASS DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4
+NC_045512.2 11301 . TA T 104.0 PASS DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4
+NC_045512.2 11812 . C CA 215.0 PASS DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3
+NC_045512.2 11812 . C A 104.0 PASS DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9
+NC_045512.2 12296 . C CA 222.0 PASS DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3
+NC_045512.2 14110 . C CA 57.0 PASS DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3
+NC_045512.2 14205 . A C 790.0 PASS DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9
+NC_045512.2 14327 . C CA 59.0 PASS DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3
+NC_045512.2 14432 . G GA 118.0 PASS DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5
+NC_045512.2 14625 . C T 78.0 PASS DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3
+NC_045512.2 14745 . TGAATTA T 111.0 PASS DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1
+NC_045512.2 14805 . C T 49314.0 PASS DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398
+NC_045512.2 14852 . TTGTA T 67.0 PASS DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3
+NC_045512.2 17916 . AT A 53.0 PASS DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3
+NC_045512.2 18350 . ATTTACC A 57.0 PASS DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3
+NC_045512.2 18688 . T C 93.0 PASS DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2
+NC_045512.2 19017 . C T 86.0 PASS DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6
+NC_045512.2 19188 . A AT 55.0 PASS DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4
+NC_045512.2 19983 . C CT 137.0 PASS DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6
+NC_045512.2 20091 . C CA 81.0 PASS DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3
+NC_045512.2 20296 . AAATT A 64.0 PASS DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3
+NC_045512.2 20890 . G GT 63.0 PASS DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2
+NC_045512.2 21101 . G GT 105.0 PASS DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6
+NC_045512.2 22383 . C CT 64.0 PASS DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4
+NC_045512.2 22583 . G GT 124.0 PASS DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5
+NC_045512.2 22802 . C CA 87.0 PASS DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3
+NC_045512.2 23191 . C T 5808.0 PASS DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96
+NC_045512.2 23568 . GTA G 66.0 PASS DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1
+NC_045512.2 23621 . G A 76.0 PASS DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5
+NC_045512.2 23735 . G GA 53.0 PASS DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3
+NC_045512.2 23835 . G GT 71.0 PASS DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5
+NC_045512.2 24025 . ACTT A 76.0 PASS DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1
+NC_045512.2 24358 . C CA 80.0 PASS DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4
+NC_045512.2 24858 . G A 74.0 PASS DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4
+NC_045512.2 24971 . G GT 61.0 PASS DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3
+NC_045512.2 25703 . C CT 54.0 PASS DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4
+NC_045512.2 26094 . TA T 78.0 PASS DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4
+NC_045512.2 26144 . G T 33850.0 PASS DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519
+NC_045512.2 27175 . C CT 63.0 PASS DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3
+NC_045512.2 27481 . C T 96.0 PASS DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2
+NC_045512.2 28147 . C CT 82.0 PASS DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4
+NC_045512.2 28214 . C CT 307.0 PASS DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5
+NC_045512.2 28214 . C T 95.0 PASS DP=891;AF=0.008979;SB=1;DP4=511,372,4,4
+NC_045512.2 29003 . C A 70.0 PASS DP=953;AF=0.006296;SB=0;DP4=401,546,2,4
+NC_045512.2 29304 . C CA 108.0 PASS DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3
+NC_045512.2 29386 . C T 84.0 PASS DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0
+NC_045512.2 29679 . CT C 70.0 PASS DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3
diff -r 000000000000 -r 2a3a00c1fa0a test-data/output.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.vcf Thu Jun 18 16:11:49 2020 -0400
@@ -0,0 +1,108 @@
+##fileformat=VCFv4.0
+##fileDate=20200606
+##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/008/613/8613450/working/pp-tmp/lofreq2_call_paralleltqdqbfki/0.vcf.gz reads.bam
+##reference=reference.fa
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FILTER=
+##FILTER= 0.001000">
+##FILTER=
+##FILTER=
+##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
+##SnpEffCmd="SnpEff -i vcf -o vcf NC_045512.2 test-data/input.vcf "
+##INFO=
+##INFO=
+##INFO=
+#CHROM POS ID REF ALT QUAL FILTER INFO
+NC_045512.2 105 . G T 3155.0 PASS DP=748;AF=0.171123;SB=0;DP4=600,20,124,4;ANN=T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.105G>T||||||
+NC_045512.2 443 . GT G 99.0 PASS DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.182delT|p.Leu61fs|182/21291|182/21291|61/7096||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.182delT|p.Leu61fs|182/540|182/540|61/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.182delT|p.Leu61fs|182/540|182/540|61/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.182delT|p.Leu61fs|182/13218|182/13218|61/4405||INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 507 . ATGGTCATGTTATGGT A 100.0 PASS DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/21291|245/21291|82/7096||INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/540|245/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/540|245/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/13218|245/13218|82/4405||INFO_REALIGN_3_PRIME
+NC_045512.2 509 . GGTCATGTTATGGTT G 99.0 PASS DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.246_259delTCATGTTATGGTTG|p.His83fs|246/21291|246/21291|82/7096||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/540|246/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/540|246/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/13218|246/13218|82/4405||INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 514 . TGTTATG T 118.0 PASS DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.253_258delATGGTT|p.Met85_Val86del|253/21291|253/21291|85/7096||INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/13218|253/13218|85/4405||INFO_REALIGN_3_PRIME
+NC_045512.2 515 . GTTATGGTT G 59.0 PASS DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.251_258delTTATGGTT|p.Val84fs|251/21291|251/21291|84/7096||,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/540|251/540|84/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/540|251/540|84/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/13218|251/13218|84/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 517 . TATG T 91.0 PASS DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.253_255delATG|p.Met85del|253/21291|253/21291|85/7096||,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.253_255delATG|p.Met85del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.253_255delATG|p.Met85del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.253_255delATG|p.Met85del|253/13218|253/13218|85/4405||
+NC_045512.2 518 . ATG A 53.0 PASS DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.254_255delTG|p.Met85fs|254/21291|254/21291|85/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/13218|254/13218|85/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 518 . ATGGTT A 78.0 PASS DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.254_258delTGGTT|p.Met85fs|254/21291|254/21291|85/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/13218|254/13218|85/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 685 . AAAGTCATTT A 60.0 PASS DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3;ANN=A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/21291|421/21291|141/7096||,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/540|421/540|141/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/540|421/540|141/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/13218|421/13218|141/4405||
+NC_045512.2 1011 . ATG A 77.0 PASS DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.747_748delTG|p.Tyr249fs|747/21291|747/21291|249/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.747_748delTG|p.Tyr249fs|747/13218|747/13218|249/4405||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.207_208delTG|p.Tyr69fs|207/1914|207/1914|69/637||WARNING_TRANSCRIPT_NO_START_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.207_208delTG|p.Tyr69fs|207/1914|207/1914|69/637||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)
+NC_045512.2 1135 . G GA 93.0 PASS DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.875dupA|p.Leu293fs|876/21291|876/21291|292/7096||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.875dupA|p.Leu293fs|876/13218|876/13218|292/4405||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.335dupA|p.Leu113fs|336/1914|336/1914|112/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.335dupA|p.Leu113fs|336/1914|336/1914|112/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.11)
+NC_045512.2 1349 . C CA 257.0 PASS DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1088dupA|p.Asn363fs|1089/21291|1089/21291|363/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1088dupA|p.Asn363fs|1089/13218|1089/13218|363/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.548dupA|p.Asn183fs|549/1914|549/1914|183/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.548dupA|p.Asn183fs|549/1914|549/1914|183/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 1730 . G A 116.0 PASS DP=997;AF=0.009027;SB=2;DP4=440,548,5,4;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1465G>A|p.Glu489Lys|1465/21291|1465/21291|489/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1465G>A|p.Glu489Lys|1465/13218|1465/13218|489/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.925G>A|p.Glu309Lys|925/1914|925/1914|309/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.925G>A|p.Glu309Lys|925/1914|925/1914|309/637||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 1946 . G GT 206.0 PASS DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1685dupT|p.Leu562fs|1686/21291|1686/21291|562/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1685dupT|p.Leu562fs|1686/13218|1686/13218|562/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1145dupT|p.Leu382fs|1146/1914|1146/1914|382/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1145dupT|p.Leu382fs|1146/1914|1146/1914|382/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 2185 . G GT 73.0 PASS DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1923dupT|p.Leu642fs|1924/21291|1924/21291|642/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1923dupT|p.Leu642fs|1924/13218|1924/13218|642/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1383dupT|p.Leu462fs|1384/1914|1384/1914|462/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1383dupT|p.Leu462fs|1384/1914|1384/1914|462/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 2310 . TA T 56.0 PASS DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2048delA|p.Asn683fs|2048/21291|2048/21291|683/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2048delA|p.Asn683fs|2048/13218|2048/13218|683/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1508delA|p.Asn503fs|1508/1914|1508/1914|503/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1508delA|p.Asn503fs|1508/1914|1508/1914|503/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 2480 . A G 49314.0 PASS DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2215A>G|p.Ile739Val|2215/21291|2215/21291|739/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2215A>G|p.Ile739Val|2215/13218|2215/13218|739/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1675A>G|p.Ile559Val|1675/1914|1675/1914|559/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1675A>G|p.Ile559Val|1675/1914|1675/1914|559/637||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 2558 . C T 49314.0 PASS DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2293C>T|p.Pro765Ser|2293/21291|2293/21291|765/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2293C>T|p.Pro765Ser|2293/13218|2293/13218|765/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1753C>T|p.Pro585Ser|1753/1914|1753/1914|585/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1753C>T|p.Pro585Ser|1753/1914|1753/1914|585/637||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 2612 . G GT 58.0 PASS DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2350dupT|p.Cys784fs|2351/21291|2351/21291|784/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2350dupT|p.Cys784fs|2351/13218|2351/13218|784/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1810dupT|p.Cys604fs|1811/1914|1811/1914|604/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1810dupT|p.Cys604fs|1811/1914|1811/1914|604/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 3259 . G T 69.0 PASS DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2994G>T|p.Gln998His|2994/21291|2994/21291|998/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2994G>T|p.Gln998His|2994/13218|2994/13218|998/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.540G>T|p.Gln180His|540/5835|540/5835|180/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.540G>T|p.Gln180His|540/5835|540/5835|180/1944||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 3412 . T TA 69.0 PASS DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3152dupA|p.Val1052fs|3153/21291|3153/21291|1051/7096||INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3152dupA|p.Val1052fs|3153/13218|3153/13218|1051/4405||INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.698dupA|p.Val234fs|699/5835|699/5835|233/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.698dupA|p.Val234fs|699/5835|699/5835|233/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 3448 . C CA 59.0 PASS DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3185dupA|p.Asn1062fs|3186/21291|3186/21291|1062/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3185dupA|p.Asn1062fs|3186/13218|3186/13218|1062/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.731dupA|p.Asn244fs|732/5835|732/5835|244/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.731dupA|p.Asn244fs|732/5835|732/5835|244/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 3545 . AATG A 57.0 PASS DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3281_3283delATG|p.Asn1094_Gly1095delinsArg|3281/21291|3281/21291|1094/7096||,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3281_3283delATG|p.Asn1094_Gly1095delinsArg|3281/13218|3281/13218|1094/4405||,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.827_829delATG|p.Asn276_Gly277delinsArg|827/5835|827/5835|276/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.827_829delATG|p.Asn276_Gly277delinsArg|827/5835|827/5835|276/1944||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 4148 . G GT 63.0 PASS DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3887dupT|p.Leu1296fs|3888/21291|3888/21291|1296/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3887dupT|p.Leu1296fs|3888/13218|3888/13218|1296/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1433dupT|p.Leu478fs|1434/5835|1434/5835|478/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1433dupT|p.Leu478fs|1434/5835|1434/5835|478/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 6287 . TG T 60.0 PASS DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6024delG|p.Trp2008fs|6024/21291|6024/21291|2008/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6024delG|p.Trp2008fs|6024/13218|6024/13218|2008/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3570delG|p.Trp1190fs|3570/5835|3570/5835|1190/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3570delG|p.Trp1190fs|3570/5835|3570/5835|1190/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 6696 . C CT 1002.0 PASS DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6435dupT|p.Leu2146fs|6436/21291|6436/21291|2146/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6435dupT|p.Leu2146fs|6436/13218|6436/13218|2146/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3981dupT|p.Leu1328fs|3982/5835|3982/5835|1328/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3981dupT|p.Leu1328fs|3982/5835|3982/5835|1328/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 6696 . C T 141.0 PASS DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6431C>T|p.Pro2144Leu|6431/21291|6431/21291|2144/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6431C>T|p.Pro2144Leu|6431/13218|6431/13218|2144/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3977C>T|p.Pro1326Leu|3977/5835|3977/5835|1326/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3977C>T|p.Pro1326Leu|3977/5835|3977/5835|1326/1944||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 7504 . C CA 57.0 PASS DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7242dupA|p.Arg2415fs|7243/21291|7243/21291|2415/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7242dupA|p.Arg2415fs|7243/13218|7243/13218|2415/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4788dupA|p.Arg1597fs|4789/5835|4789/5835|1597/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4788dupA|p.Arg1597fs|4789/5835|4789/5835|1597/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 9118 . C T 170.0 PASS DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8853C>T|p.Asp2951Asp|8853/21291|8853/21291|2951/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8853C>T|p.Asp2951Asp|8853/13218|8853/13218|2951/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.564C>T|p.Asp188Asp|564/1500|564/1500|188/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.564C>T|p.Asp188Asp|564/1500|564/1500|188/499||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 9502 . C T 221.0 PASS DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9237C>T|p.Ala3079Ala|9237/21291|9237/21291|3079/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9237C>T|p.Ala3079Ala|9237/13218|9237/13218|3079/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.948C>T|p.Ala316Ala|948/1500|948/1500|316/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.948C>T|p.Ala316Ala|948/1500|948/1500|316/499||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 9701 . AT A 59.0 PASS DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9439delT|p.Cys3147fs|9439/21291|9439/21291|3147/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9439delT|p.Cys3147fs|9439/13218|9439/13218|3147/4405||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1150delT|p.Cys384fs|1150/1500|1150/1500|384/499||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1150delT|p.Cys384fs|1150/1500|1150/1500|384/499||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 10605 . C CT 116.0 PASS DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10344dupT|p.Val3449fs|10345/21291|10345/21291|3449/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10344dupT|p.Val3449fs|10345/13218|10345/13218|3449/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.555dupT|p.Val186fs|556/918|556/918|186/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.555dupT|p.Val186fs|556/918|556/918|186/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 10619 . C A 235.0 PASS DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10354C>A|p.Gln3452Lys|10354/21291|10354/21291|3452/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10354C>A|p.Gln3452Lys|10354/13218|10354/13218|3452/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.565C>A|p.Gln189Lys|565/918|565/918|189/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.565C>A|p.Gln189Lys|565/918|565/918|189/305||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 10660 . TA T 122.0 PASS DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10397delA|p.Asn3466fs|10397/21291|10397/21291|3466/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10397delA|p.Asn3466fs|10397/13218|10397/13218|3466/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.608delA|p.Asn203fs|608/918|608/918|203/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.608delA|p.Asn203fs|608/918|608/918|203/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 11074 . C CT 281.0 PASS DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817dupT|p.Leu3606fs|10818/21291|10818/21291|3606/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817dupT|p.Leu3606fs|10818/13218|10818/13218|3606/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 11082 . TG T 1843.0 PASS DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10818delG|p.Leu3606fs|10818/21291|10818/21291|3606/7096||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10818delG|p.Leu3606fs|10818/13218|10818/13218|3606/4405||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.111delG|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.111delG|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 11083 . G T 39536.0 PASS DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10818G>T|p.Leu3606Phe|10818/21291|10818/21291|3606/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10818G>T|p.Leu3606Phe|10818/13218|10818/13218|3606/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.111G>T|p.Leu37Phe|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.111G>T|p.Leu37Phe|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 11133 . CT C 60.0 PASS DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4;ANN=C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10872delT|p.Phe3624fs|10872/21291|10872/21291|3624/7096||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10872delT|p.Phe3624fs|10872/13218|10872/13218|3624/4405||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.165delT|p.Phe55fs|165/870|165/870|55/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.165delT|p.Phe55fs|165/870|165/870|55/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 11301 . TA T 104.0 PASS DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11040delA|p.Asp3681fs|11040/21291|11040/21291|3680/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11040delA|p.Asp3681fs|11040/13218|11040/13218|3680/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.333delA|p.Asp112fs|333/870|333/870|111/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.333delA|p.Asp112fs|333/870|333/870|111/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 11812 . C CA 215.0 PASS DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11550dupA|p.Pro3851fs|11551/21291|11551/21291|3851/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11550dupA|p.Pro3851fs|11551/13218|11551/13218|3851/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.843dupA|p.Pro282fs|844/870|844/870|282/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.843dupA|p.Pro282fs|844/870|844/870|282/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 11812 . C A 104.0 PASS DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11547C>A|p.Gly3849Gly|11547/21291|11547/21291|3849/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11547C>A|p.Gly3849Gly|11547/13218|11547/13218|3849/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.840C>A|p.Gly280Gly|840/870|840/870|280/289||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.840C>A|p.Gly280Gly|840/870|840/870|280/289||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 12296 . C CA 222.0 PASS DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12034dupA|p.Met4012fs|12035/21291|12035/21291|4012/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12034dupA|p.Met4012fs|12035/13218|12035/13218|4012/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.208dupA|p.Met70fs|209/594|209/594|70/197||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.208dupA|p.Met70fs|209/594|209/594|70/197||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14)
+NC_045512.2 14110 . C CA 57.0 PASS DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13849dupA|p.Thr4617fs|13850/21291|13850/21291|4617/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.673dupA|p.Thr225fs|674/2796|674/2796|225/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 14205 . A C 790.0 PASS DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13941A>C|p.Ser4647Ser|13941/21291|13941/21291|4647/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.765A>C|p.Ser255Ser|765/2796|765/2796|255/931||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 14327 . C CA 59.0 PASS DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14066dupA|p.Asn4689fs|14067/21291|14067/21291|4689/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.890dupA|p.Asn297fs|891/2796|891/2796|297/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 14432 . G GA 118.0 PASS DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14173dupA|p.Ile4725fs|14174/21291|14174/21291|4725/7096||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.997dupA|p.Ile333fs|998/2796|998/2796|333/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 14625 . C T 78.0 PASS DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14361C>T|p.Cys4787Cys|14361/21291|14361/21291|4787/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1185C>T|p.Cys395Cys|1185/2796|1185/2796|395/931||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 14745 . TGAATTA T 111.0 PASS DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14482_14487delGAATTA|p.Glu4828_Leu4829del|14482/21291|14482/21291|4828/7096||,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1306_1311delGAATTA|p.Glu436_Leu437del|1306/2796|1306/2796|436/931||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 14805 . C T 49314.0 PASS DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14541C>T|p.Tyr4847Tyr|14541/21291|14541/21291|4847/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1365C>T|p.Tyr455Tyr|1365/2796|1365/2796|455/931||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 14852 . TTGTA T 67.0 PASS DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14589_14592delTGTA|p.Phe4863fs|14589/21291|14589/21291|4863/7096||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1413_1416delTGTA|p.Phe471fs|1413/2796|1413/2796|471/931||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 17916 . AT A 53.0 PASS DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17655delT|p.Phe5885fs|17655/21291|17655/21291|5885/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1683delT|p.Phe561fs|1683/1803|1683/1803|561/600||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 18350 . ATTTACC A 57.0 PASS DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18092_18097delCTTTAC|p.Pro6031_Leu6032del|18092/21291|18092/21291|6031/7096||INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.317_322delCTTTAC|p.Pro106_Leu107del|317/1581|317/1581|106/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME
+NC_045512.2 18688 . T C 93.0 PASS DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18424T>C|p.Phe6142Leu|18424/21291|18424/21291|6142/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.649T>C|p.Phe217Leu|649/1581|649/1581|217/526||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 19017 . C T 86.0 PASS DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18753C>T|p.Phe6251Phe|18753/21291|18753/21291|6251/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.978C>T|p.Phe326Phe|978/1581|978/1581|326/526||WARNING_TRANSCRIPT_NO_START_CODON
+NC_045512.2 19188 . A AT 55.0 PASS DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4;ANN=AT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18928dupT|p.Trp6310fs|18929/21291|18929/21291|6310/7096||INFO_REALIGN_3_PRIME,AT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1153dupT|p.Trp385fs|1154/1581|1154/1581|385/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 19983 . C CT 137.0 PASS DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6;ANN=CT|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19725dupT|p.Asp6576fs|19726/21291|19726/21291|6576/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.369dupT|p.Asp124fs|370/1038|370/1038|124/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 20091 . C CA 81.0 PASS DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19830dupA|p.Gln6611fs|19831/21291|19831/21291|6611/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.474dupA|p.Gln159fs|475/1038|475/1038|159/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 20296 . AAATT A 64.0 PASS DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20034_20037delATTA|p.Leu6679fs|20034/21291|20034/21291|6678/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.678_681delATTA|p.Leu227fs|678/1038|678/1038|226/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07)
+NC_045512.2 20890 . G GT 63.0 PASS DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20628dupT|p.Ala6877fs|20629/21291|20629/21291|6877/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.234dupT|p.Ala79fs|235/894|235/894|79/297||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.04)
+NC_045512.2 21101 . G GT 105.0 PASS DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20843dupT|p.Thr6949fs|20844/21291|20844/21291|6948/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.449dupT|p.Thr151fs|450/894|450/894|150/297||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.04)
+NC_045512.2 22383 . C CT 64.0 PASS DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.825dupT|p.Leu276fs|826/3822|826/3822|276/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 22583 . G GT 124.0 PASS DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5;ANN=GT|frameshift_variant&stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1026dupT|p.Asn343fs|1027/3822|1027/3822|343/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 22802 . C CA 87.0 PASS DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1243dupA|p.Thr415fs|1244/3822|1244/3822|415/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 23191 . C T 5808.0 PASS DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1629C>T|p.Phe543Phe|1629/3822|1629/3822|543/1273||
+NC_045512.2 23568 . GTA G 66.0 PASS DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1;ANN=G|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2010_2011delAT|p.Ile670fs|2010/3822|2010/3822|670/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 23621 . G A 76.0 PASS DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2059G>A|p.Val687Ile|2059/3822|2059/3822|687/1273||
+NC_045512.2 23735 . G GA 53.0 PASS DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3;ANN=GA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2176dupA|p.Ile726fs|2177/3822|2177/3822|726/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 23835 . G GT 71.0 PASS DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5;ANN=GT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2278dupT|p.Cys760fs|2279/3822|2279/3822|760/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 24025 . ACTT A 76.0 PASS DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1;ANN=A|conservative_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2464_2466delCTT|p.Leu822del|2464/3822|2464/3822|822/1273||
+NC_045512.2 24358 . C CA 80.0 PASS DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2800dupA|p.Ile934fs|2801/3822|2801/3822|934/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 24858 . G A 74.0 PASS DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3296G>A|p.Gly1099Asp|3296/3822|3296/3822|1099/1273||
+NC_045512.2 24971 . G GT 61.0 PASS DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3412dupT|p.Tyr1138fs|3413/3822|3413/3822|1138/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00)
+NC_045512.2 25703 . C CT 54.0 PASS DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.315dupT|p.Leu106fs|316/828|316/828|106/275||INFO_REALIGN_3_PRIME;LOF=(ORF3a|GU280_gp03|1|1.00)
+NC_045512.2 26094 . TA T 78.0 PASS DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4;ANN=T|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.706delA|p.Ile236fs|706/828|706/828|236/275||INFO_REALIGN_3_PRIME;LOF=(ORF3a|GU280_gp03|1|1.00)
+NC_045512.2 26144 . G T 33850.0 PASS DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.752G>T|p.Gly251Val|752/828|752/828|251/275||
+NC_045512.2 27175 . C CT 63.0 PASS DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3;ANN=CT|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.656dupT|p.Leu219fs|657/669|657/669|219/222||INFO_REALIGN_3_PRIME
+NC_045512.2 27481 . C T 96.0 PASS DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.88C>T|p.Leu30Phe|88/366|88/366|30/121||
+NC_045512.2 28147 . C CT 82.0 PASS DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.258dupT|p.Thr87fs|259/366|259/366|87/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|GU280_gp09|1|1.00)
+NC_045512.2 28214 . C CT 307.0 PASS DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5;ANN=CT|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.326dupT|p.Leu109fs|327/366|327/366|109/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|GU280_gp09|1|1.00)
+NC_045512.2 28214 . C T 95.0 PASS DP=891;AF=0.008979;SB=1;DP4=511,372,4,4;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.321C>T|p.Asp107Asp|321/366|321/366|107/121||
+NC_045512.2 29003 . C A 70.0 PASS DP=953;AF=0.006296;SB=0;DP4=401,546,2,4;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.730C>A|p.Gln244Lys|730/1260|730/1260|244/419||
+NC_045512.2 29304 . C CA 108.0 PASS DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1034dupA|p.Asn345fs|1035/1260|1035/1260|345/419||INFO_REALIGN_3_PRIME;LOF=(N|GU280_gp10|1|1.00)
+NC_045512.2 29386 . C T 84.0 PASS DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1113C>T|p.Asp371Asp|1113/1260|1113/1260|371/419||
+NC_045512.2 29679 . CT C 70.0 PASS DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3;ANN=C|intergenic_region|MODIFIER|ORF10-CHR_END|GU280_gp11-CHR_END|intergenic_region|GU280_gp11-CHR_END|||n.29680delT||||||