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changeset 0:f079716f598c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
author iuc
date Wed, 31 May 2023 17:10:11 +0000
parents
children 029d90b0c4f6
files frameshift_deletions_checks.xml macros.xml test-data/Genes_NC_045512.2.GFF3 test-data/NC_045512.2.fasta.gz test-data/REF_aln_trim.cram test-data/REF_aln_trim.cram.crai test-data/consensus.bcftools.fasta.gz test-data/frameshift_deletions_check.tsv
diffstat 8 files changed, 280 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frameshift_deletions_checks.xml	Wed May 31 17:10:11 2023 +0000
@@ -0,0 +1,89 @@
+<tool id="smgu_frameshift_deletions_checks" name="Frameshift Deletions Checks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>reports on frameshifting indels in consensus sequence</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">smallgenomeutilities</requirement>
+    </requirements>
+    <!-- once we have version-from-git-tag in 0.4.0: <version_command>frameshift_deletion_checks &#x002D&#x002Dversion</version_command> -->
+    <command detect_errors="exit_code">
+    <![CDATA[
+#if $input.is_of_type("cram"):
+echo 'is CRAM' >&2 &&
+ ln -vs '$input' 'input.${input.ext}' >&2 &&
+ ln -vs '$input.metadata.cram_index' 'input.${input.ext}.crai' >&2 &&
+#elif $input.is_of_type("bam"):
+ echo 'is BAM' &&
+ ln -s '$input' 'input.${input.ext}' >&2 &&
+ ln -s '$input.metadata.bam_index' 'input.${input.ext}.bai' >&2 &&
+#else:
+# raise TypeError('Unknown input alignment type ${input.ext}')
+#end if
+ln -vs '$consensus' 'consensus.${consensus.ext}' >&2 &&
+ln -vs '$reference' 'reference.${reference.ext}' >&2 &&
+
+frameshift_deletions_checks 
+    --input='input.${input.ext}'
+    --consensus='consensus.${consensus.ext}'
+    --reference='reference.${reference.ext}'
+    --genes='$genes'
+    --output='$report' 
+#if $orf1ab != '':
+    --orf1ab='$orf1ab'
+#end if
+    '$english'
+    $zero_based
+]]>
+    <!-- ##cores \${GALAXY_SLOTS:-4} -->
+    </command>
+    <inputs>
+        <param argument="--consensus" type="data" format="fasta" label="Consensus" help="Fasta file containing the sample's consensus sequence (majority, with indels)" />
+        <param argument="--input" type="data" format="bam,cram" label="Input BAM" help="Input BAM file with sample's sequencing reads, aligned against the reference" />
+        <param argument="--reference" type="data" format="fasta" label="Reference" help="Fasta file containing the reference sequence (used during alignment) to compare against" />
+        <param argument="--genes" type="data" format="gff" label="Genes GFF" help="GFF file listing genes positions on the reference sequence" />
+        
+        <param argument="--english" type="boolean" truevalue="--english" falsevalue="--no-english" checked="true" optional="true" label="Write Summary Diagnosis?" help="If checked writes english summary diagnosis." />
+        <param argument="--zero-based" type="boolean" truevalue="--zero-based" falsevalue="" checked="false" optional="true" label="Use 0-based Sequence Positions?" help="Use 0-based (python) instead of 1-based (standard) seq positions" />
+        <param argument="--orf1ab" type="text" value="cds-YP_009724389.1" optional="true" label="ORF1AB" help="CDS ID for the full Orf1ab CDS, comprising the ribosomal shift. In the GFF this CDS should consist of 2 entries with the same CDS ID due to the partial overlap caused by the ribosomal shift at translation time."/>
+    </inputs>
+    <outputs>
+        <data name="report" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="consensus" value="consensus.bcftools.fasta.gz" />
+            <param name="input" value="REF_aln_trim.cram" />
+            <param name="reference" value="NC_045512.2.fasta.gz" />
+            <param name="genes" value="Genes_NC_045512.2.GFF3" />
+            <output name="report" value="frameshift_deletions_check.tsv" />
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+Produces a report about frameshifting indels in a consensus sequences.
+
+Developed as part of the `V-pipe workflow for analysing NGS data of short viral genomes <https://github.com/cbg-ethz/V-pipe>`_.
+
+Columns signification:
+----------------------
+
+* *gene_region*: Gene in which the deletion is found according to ``--genes`` argument;
+* *reads_all*: Total number of reads covering the indel;
+* *reads_fwd*: Total nubmer of forward reads covering the indel;
+* *reads_rev*: Total nubmer of reverse reads covering the indel;
+* *deletions/insertions*: Number of reads supporting the deletion/insertion;
+* *freq_del/freq_insert*: Fraction of reads supporting the deletion/insertion;
+* *matches_ref*: number of reads that matche with the reference base;
+* *pos_critical_inserts*: Start positions of insertions in the same gene_region that occur in > 40% of reads;
+* *pos_critical_dels*: Start positions of deletions in the same gene_region that occur in > 40% of reads;
+* *homopolymeric*: True if either around the start or end position of the deletion three bases are the same, which may have caused the polymerase to skip during reverse transcription of viral RNA to cDNA, e.g. AATAG;
+* *ref_base*: base in the reference genome;
+* *indel_position_english*: english sentence describing the indel;
+* *indel_diagnosis*: english sentence with the indel diagnosis;
+* *orf1ab*: CDS ID for the full Orf1ab CDS, comprising the ribosomal shift. In the GFF this CDS should consist of 2 entries with the same CDS ID due to the parital overlap caused by the ribosomal shift at translation time
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 31 17:10:11 2023 +0000
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.3.9</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.09</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">v-pipe</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btab015</citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Genes_NC_045512.2.GFF3	Wed May 31 17:10:11 2023 +0000
@@ -0,0 +1,36 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_045512.2 1 29903
+NC_045512.2	RefSeq	five_prime_UTR	1	265	.	+	.	ID=id-NC_045512.2:1..265;gbkey=5'UTR
+NC_045512.2	RefSeq	gene	266	21555	.	+	.	ID=gene-GU280_gp01;Dbxref=GeneID:43740578;Name=ORF1ab;gbkey=Gene;gene=ORF1ab;gene_biotype=protein_coding;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	CDS	266	13468	.	+	1	ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=Genbank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
+NC_045512.2	RefSeq	CDS	13468	21555	.	+	1	ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=Genbank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab%3B translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1
+NC_045512.2	RefSeq	CDS	266	13483	.	+	1	ID=cds-YP_009725295.1;Parent=gene-GU280_gp01;Dbxref=Genbank:YP_009725295.1,GeneID:43740578;Name=YP_009725295.1;Note=pp1a;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1a polyprotein;protein_id=YP_009725295.1
+NC_045512.2	RefSeq	stem_loop	13476	13503	.	+	.	ID=id-GU280_gp01;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 1;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	stem_loop	13488	13542	.	+	.	ID=id-GU280_gp01-2;Dbxref=GeneID:43740578;function=Coronavirus frameshifting stimulation element stem-loop 2;gbkey=stem_loop;gene=ORF1ab;inference=COORDINATES: profile:profile:Rfam-release-14.1:RF00507%2CInfernal:1.1.2;locus_tag=GU280_gp01
+NC_045512.2	RefSeq	gene	21563	25384	.	+	.	ID=gene-GU280_gp02;Dbxref=GeneID:43740568;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;locus_tag=GU280_gp02
+NC_045512.2	RefSeq	CDS	21563	25384	.	+	1	ID=cds-YP_009724390.1;Parent=gene-GU280_gp02;Dbxref=Genbank:YP_009724390.1,GeneID:43740568;Name=YP_009724390.1;Note=structural protein%3B spike protein;gbkey=CDS;gene=S;locus_tag=GU280_gp02;product=surface glycoprotein;protein_id=YP_009724390.1
+NC_045512.2	RefSeq	gene	25393	26220	.	+	.	ID=gene-GU280_gp03;Dbxref=GeneID:43740569;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;locus_tag=GU280_gp03
+NC_045512.2	RefSeq	CDS	25393	26220	.	+	1	ID=cds-YP_009724391.1;Parent=gene-GU280_gp03;Dbxref=Genbank:YP_009724391.1,GeneID:43740569;Name=YP_009724391.1;gbkey=CDS;gene=ORF3a;locus_tag=GU280_gp03;product=ORF3a protein;protein_id=YP_009724391.1
+NC_045512.2	RefSeq	gene	26245	26472	.	+	.	ID=gene-GU280_gp04;Dbxref=GeneID:43740570;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;locus_tag=GU280_gp04
+NC_045512.2	RefSeq	CDS	26245	26472	.	+	1	ID=cds-YP_009724392.1;Parent=gene-GU280_gp04;Dbxref=Genbank:YP_009724392.1,GeneID:43740570;Name=YP_009724392.1;Note=ORF4%3B structural protein%3B E protein;gbkey=CDS;gene=E;locus_tag=GU280_gp04;product=envelope protein;protein_id=YP_009724392.1
+NC_045512.2	RefSeq	gene	26523	27191	.	+	.	ID=gene-GU280_gp05;Dbxref=GeneID:43740571;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;locus_tag=GU280_gp05
+NC_045512.2	RefSeq	CDS	26523	27191	.	+	1	ID=cds-YP_009724393.1;Parent=gene-GU280_gp05;Dbxref=Genbank:YP_009724393.1,GeneID:43740571;Name=YP_009724393.1;Note=ORF5%3B structural protein;gbkey=CDS;gene=M;locus_tag=GU280_gp05;product=membrane glycoprotein;protein_id=YP_009724393.1
+NC_045512.2	RefSeq	gene	27202	27387	.	+	.	ID=gene-GU280_gp06;Dbxref=GeneID:43740572;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;locus_tag=GU280_gp06
+NC_045512.2	RefSeq	CDS	27202	27387	.	+	1	ID=cds-YP_009724394.1;Parent=gene-GU280_gp06;Dbxref=Genbank:YP_009724394.1,GeneID:43740572;Name=YP_009724394.1;gbkey=CDS;gene=ORF6;locus_tag=GU280_gp06;product=ORF6 protein;protein_id=YP_009724394.1
+NC_045512.2	RefSeq	gene	27394	27759	.	+	.	ID=gene-GU280_gp07;Dbxref=GeneID:43740573;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;locus_tag=GU280_gp07
+NC_045512.2	RefSeq	CDS	27394	27759	.	+	1	ID=cds-YP_009724395.1;Parent=gene-GU280_gp07;Dbxref=Genbank:YP_009724395.1,GeneID:43740573;Name=YP_009724395.1;gbkey=CDS;gene=ORF7a;locus_tag=GU280_gp07;product=ORF7a protein;protein_id=YP_009724395.1
+NC_045512.2	RefSeq	gene	27756	27887	.	+	.	ID=gene-GU280_gp08;Dbxref=GeneID:43740574;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;locus_tag=GU280_gp08
+NC_045512.2	RefSeq	CDS	27756	27887	.	+	1	ID=cds-YP_009725318.1;Parent=gene-GU280_gp08;Dbxref=Genbank:YP_009725318.1,GeneID:43740574;Name=YP_009725318.1;gbkey=CDS;gene=ORF7b;locus_tag=GU280_gp08;product=ORF7b;protein_id=YP_009725318.1
+NC_045512.2	RefSeq	gene	27894	28259	.	+	.	ID=gene-GU280_gp09;Dbxref=GeneID:43740577;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;locus_tag=GU280_gp09
+NC_045512.2	RefSeq	CDS	27894	28259	.	+	1	ID=cds-YP_009724396.1;Parent=gene-GU280_gp09;Dbxref=Genbank:YP_009724396.1,GeneID:43740577;Name=YP_009724396.1;gbkey=CDS;gene=ORF8;locus_tag=GU280_gp09;product=ORF8 protein;protein_id=YP_009724396.1
+NC_045512.2	RefSeq	gene	28274	29533	.	+	.	ID=gene-GU280_gp10;Dbxref=GeneID:43740575;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;locus_tag=GU280_gp10
+NC_045512.2	RefSeq	CDS	28274	29533	.	+	1	ID=cds-YP_009724397.2;Parent=gene-GU280_gp10;Dbxref=Genbank:YP_009724397.2,GeneID:43740575;Name=YP_009724397.2;Note=ORF9%3B structural protein;gbkey=CDS;gene=N;locus_tag=GU280_gp10;product=nucleocapsid phosphoprotein;protein_id=YP_009724397.2
+NC_045512.2	RefSeq	gene	29558	29674	.	+	.	ID=gene-GU280_gp11;Dbxref=GeneID:43740576;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	CDS	29558	29674	.	+	1	ID=cds-YP_009725255.1;Parent=gene-GU280_gp11;Dbxref=Genbank:YP_009725255.1,GeneID:43740576;Name=YP_009725255.1;gbkey=CDS;gene=ORF10;locus_tag=GU280_gp11;product=ORF10 protein;protein_id=YP_009725255.1
+NC_045512.2	RefSeq	stem_loop	29609	29644	.	+	.	ID=id-GU280_gp11;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 1;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	stem_loop	29629	29657	.	+	.	ID=id-GU280_gp11-2;Dbxref=GeneID:43740576;function=Coronavirus 3' UTR pseudoknot stem-loop 2;gbkey=stem_loop;gene=ORF10;inference=COORDINATES: profile::Rfam-release-14.1:RF00165%2CInfernal:1.1.2;locus_tag=GU280_gp11
+NC_045512.2	RefSeq	three_prime_UTR	29675	29903	.	+	.	ID=id-NC_045512.2:29675..29903;gbkey=3'UTR
+NC_045512.2	RefSeq	stem_loop	29728	29768	.	+	.	ID=id-NC_045512.2:29728..29768;Note=basepair exception: alignment to the Rfam model implies coordinates 29740:29758 form a noncanonical C:T basepair%2C but the homologous positions form a highly conserved C:G basepair in other viruses%2C including SARS (NC_004718.3);function=Coronavirus 3' stem-loop II-like motif (s2m);gbkey=stem_loop;inference=COORDINATES: profile:Rfam-release-14.1:RF00164%2CInfernal:1.1.2
+###
Binary file test-data/NC_045512.2.fasta.gz has changed
Binary file test-data/REF_aln_trim.cram has changed
Binary file test-data/REF_aln_trim.cram.crai has changed
Binary file test-data/consensus.bcftools.fasta.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/frameshift_deletions_check.tsv	Wed May 31 17:10:11 2023 +0000
@@ -0,0 +1,140 @@
+	ref_id	start_position	length	VARIANT	gene_region	reads_all	reads_fwd	reads_rev	deletions	freq_del	freq_del_fwd	freq_del_rev	deletions_fwd	deletions_rev	insertions	freq_insert	freq_insert_fwd	freq_insert_rev	insertions_fwd	insertions_rev	stops	freq_stop	freq_stop_fwd	freq_stop_rev	stops_fwd	stops_rev	matches_ref	pos_critical_inserts	pos_critical_dels	homopolymeric	ref_base	cons_id	variant_position_english	variant_diagnosis
+0	NC_045512.2	5600	2	deletion	ORF1ab	40	40	0	23	0.575	0.575	0	23	0	0	0.0	0.0	0	0	0	0	0	0	0	0	0	17	[21101]	[8740, 18800]	1	b'T'	NC_045512.2	Gap of 2 nucleotide(s) found at refpos 5600	only fwd or rev reads available, deletion supported by the majority of them; homopolymeric; neighboring indels may restore reading frame
+1	NC_045512.2	5602	3	stopgain	ORF1ab	40	40	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	40	1.0	1.0	0	40	0	40	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5602, aminoacid position 1779	only fwd or rev reads available, stopgain supported by the majority of them
+2	NC_045512.2	5635	3	stopgain	ORF1ab	40	40	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	40	1.0	1.0	0	40	0	40	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5635, aminoacid position 1790	only fwd or rev reads available, stopgain supported by the majority of them
+3	NC_045512.2	5707	3	stopgain	ORF1ab	63	39	24	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	63	1.0	1.0	1.0	39	24	63	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5707, aminoacid position 1814	stopgain supported by majority of fwd and rev reads
+4	NC_045512.2	5713	3	stopgain	ORF1ab	72	39	33	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	72	1.0	1.0	1.0	39	33	72	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5713, aminoacid position 1816	stopgain supported by majority of fwd and rev reads
+5	NC_045512.2	5737	3	stopgain	ORF1ab	79	39	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	79	1.0	1.0	1.0	39	40	79	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5737, aminoacid position 1824	stopgain supported by majority of fwd and rev reads
+6	NC_045512.2	5740	3	stopgain	ORF1ab	79	39	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	79	1.0	1.0	1.0	39	40	79	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5740, aminoacid position 1825	stopgain supported by majority of fwd and rev reads
+7	NC_045512.2	5752	3	stopgain	ORF1ab	79	39	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	79	1.0	1.0	1.0	39	40	79	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5752, aminoacid position 1829	stopgain supported by majority of fwd and rev reads
+8	NC_045512.2	5773	3	stopgain	ORF1ab	78	38	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	78	1.0	1.0	1.0	38	40	78	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5773, aminoacid position 1836	stopgain supported by majority of fwd and rev reads
+9	NC_045512.2	5788	3	stopgain	ORF1ab	74	34	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	74	1.0	1.0	1.0	34	40	74	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5788, aminoacid position 1841	stopgain supported by majority of fwd and rev reads
+10	NC_045512.2	5911	3	stopgain	ORF1ab	45	5	40	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	45	1.0	1.0	1.0	5	40	45	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 5911, aminoacid position 1882	stopgain supported by majority of fwd and rev reads
+11	NC_045512.2	6043	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6043, aminoacid position 1926	stopgain supported by majority of fwd and rev reads
+12	NC_045512.2	6049	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6049, aminoacid position 1928	stopgain supported by majority of fwd and rev reads
+13	NC_045512.2	6061	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6061, aminoacid position 1932	stopgain supported by majority of fwd and rev reads
+14	NC_045512.2	6064	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6064, aminoacid position 1933	stopgain supported by majority of fwd and rev reads
+15	NC_045512.2	6079	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6079, aminoacid position 1938	stopgain supported by majority of fwd and rev reads
+16	NC_045512.2	6082	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6082, aminoacid position 1939	stopgain supported by majority of fwd and rev reads
+17	NC_045512.2	6106	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6106, aminoacid position 1947	stopgain supported by majority of fwd and rev reads
+18	NC_045512.2	6202	3	stopgain	ORF1ab	86	81	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	81	5	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6202, aminoacid position 1979	stopgain supported by majority of fwd and rev reads
+19	NC_045512.2	6214	3	stopgain	ORF1ab	86	81	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	81	5	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6214, aminoacid position 1983	stopgain supported by majority of fwd and rev reads
+20	NC_045512.2	6226	3	stopgain	ORF1ab	86	81	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	81	5	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6226, aminoacid position 1987	stopgain supported by majority of fwd and rev reads
+21	NC_045512.2	6247	3	stopgain	ORF1ab	86	81	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	81	5	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6247, aminoacid position 1994	stopgain supported by majority of fwd and rev reads
+22	NC_045512.2	6259	3	stopgain	ORF1ab	81	81	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	81	1.0	1.0	0	81	0	81	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6259, aminoacid position 1998	only fwd or rev reads available, stopgain supported by the majority of them
+23	NC_045512.2	6262	3	stopgain	ORF1ab	81	81	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	81	1.0	1.0	0	81	0	81	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6262, aminoacid position 1999	only fwd or rev reads available, stopgain supported by the majority of them
+24	NC_045512.2	6274	3	stopgain	ORF1ab	80	80	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	80	1.0	1.0	0	80	0	80	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6274, aminoacid position 2003	only fwd or rev reads available, stopgain supported by the majority of them
+25	NC_045512.2	6322	3	stopgain	ORF1ab	153	80	73	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	153	1.0	1.0	1.0	80	73	153	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6322, aminoacid position 2019	stopgain supported by majority of fwd and rev reads
+26	NC_045512.2	6340	3	stopgain	ORF1ab	157	80	77	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	157	1.0	1.0	1.0	80	77	157	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6340, aminoacid position 2025	stopgain supported by majority of fwd and rev reads
+27	NC_045512.2	6376	3	stopgain	ORF1ab	157	78	79	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	157	1.0	1.0	1.0	78	79	157	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6376, aminoacid position 2037	stopgain supported by majority of fwd and rev reads
+28	NC_045512.2	6409	3	stopgain	ORF1ab	152	71	81	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	152	1.0	1.0	1.0	71	81	152	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6409, aminoacid position 2048	stopgain supported by majority of fwd and rev reads
+29	NC_045512.2	6451	3	stopgain	ORF1ab	81	0	81	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	81	1.0	0	1.0	0	81	81	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6451, aminoacid position 2062	only fwd or rev reads available, stopgain supported by the majority of them
+30	NC_045512.2	6457	3	stopgain	ORF1ab	81	0	81	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	81	1.0	0	1.0	0	81	81	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6457, aminoacid position 2064	only fwd or rev reads available, stopgain supported by the majority of them
+31	NC_045512.2	6496	3	stopgain	ORF1ab	86	5	81	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	5	81	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6496, aminoacid position 2077	stopgain supported by majority of fwd and rev reads
+32	NC_045512.2	6508	3	stopgain	ORF1ab	86	5	81	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	5	81	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6508, aminoacid position 2081	stopgain supported by majority of fwd and rev reads
+33	NC_045512.2	6511	3	stopgain	ORF1ab	86	5	81	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	86	1.0	1.0	1.0	5	81	86	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6511, aminoacid position 2082	stopgain supported by majority of fwd and rev reads
+34	NC_045512.2	6655	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6655, aminoacid position 2130	stopgain supported by majority of fwd and rev reads
+35	NC_045512.2	6658	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6658, aminoacid position 2131	stopgain supported by majority of fwd and rev reads
+36	NC_045512.2	6682	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6682, aminoacid position 2139	stopgain supported by majority of fwd and rev reads
+37	NC_045512.2	6691	3	stopgain	ORF1ab	10	5	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	10	1.0	1.0	1.0	5	5	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 6691, aminoacid position 2142	stopgain supported by majority of fwd and rev reads
+38	NC_045512.2	7342	3	stopgain	ORF1ab	173	169	4	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	173	1.0	1.0	1.0	169	4	173	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7342, aminoacid position 2359	stopgain supported by majority of fwd and rev reads
+39	NC_045512.2	7345	3	stopgain	ORF1ab	173	169	4	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	173	1.0	1.0	1.0	169	4	173	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7345, aminoacid position 2360	stopgain supported by majority of fwd and rev reads
+40	NC_045512.2	7372	3	stopgain	ORF1ab	173	169	4	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	173	1.0	1.0	1.0	169	4	173	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7372, aminoacid position 2369	stopgain supported by majority of fwd and rev reads
+41	NC_045512.2	7408	3	stopgain	ORF1ab	168	168	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	168	1.0	1.0	0	168	0	168	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7408, aminoacid position 2381	only fwd or rev reads available, stopgain supported by the majority of them
+42	NC_045512.2	7477	3	stopgain	ORF1ab	330	167	163	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	330	1.0	1.0	1.0	167	163	330	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7477, aminoacid position 2404	stopgain supported by majority of fwd and rev reads
+43	NC_045512.2	7510	3	stopgain	ORF1ab	334	166	168	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	334	1.0	1.0	1.0	166	168	334	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7510, aminoacid position 2415	stopgain supported by majority of fwd and rev reads
+44	NC_045512.2	7513	3	stopgain	ORF1ab	333	165	168	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	333	1.0	1.0	1.0	165	168	333	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7513, aminoacid position 2416	stopgain supported by majority of fwd and rev reads
+45	NC_045512.2	7546	3	stopgain	ORF1ab	309	141	168	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	309	1.0	1.0	1.0	141	168	309	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7546, aminoacid position 2427	stopgain supported by majority of fwd and rev reads
+46	NC_045512.2	7555	3	stopgain	ORF1ab	289	121	168	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	289	1.0	1.0	1.0	121	168	289	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7555, aminoacid position 2430	stopgain supported by majority of fwd and rev reads
+47	NC_045512.2	7579	3	stopgain	ORF1ab	169	0	169	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	169	1.0	0	1.0	0	169	169	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7579, aminoacid position 2438	only fwd or rev reads available, stopgain supported by the majority of them
+48	NC_045512.2	7588	3	stopgain	ORF1ab	169	0	169	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	169	1.0	0	1.0	0	169	169	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7588, aminoacid position 2441	only fwd or rev reads available, stopgain supported by the majority of them
+49	NC_045512.2	7624	3	stopgain	ORF1ab	170	0	170	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	170	1.0	0	1.0	0	170	170	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7624, aminoacid position 2453	only fwd or rev reads available, stopgain supported by the majority of them
+50	NC_045512.2	7630	3	stopgain	ORF1ab	170	0	170	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	170	1.0	0	1.0	0	170	170	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7630, aminoacid position 2455	only fwd or rev reads available, stopgain supported by the majority of them
+51	NC_045512.2	7648	3	stopgain	ORF1ab	170	0	170	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	170	1.0	0	1.0	0	170	170	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7648, aminoacid position 2461	only fwd or rev reads available, stopgain supported by the majority of them
+52	NC_045512.2	7660	3	stopgain	ORF1ab	176	6	170	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	176	1.0	1.0	1.0	6	170	176	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7660, aminoacid position 2465	stopgain supported by majority of fwd and rev reads
+53	NC_045512.2	7663	3	stopgain	ORF1ab	176	6	170	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	173	0.9829545454545454	1.0	0.9823529411764705	6	167	173	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7663, aminoacid position 2466	stopgain supported by majority of fwd and rev reads
+54	NC_045512.2	7666	3	stopgain	ORF1ab	176	6	170	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	176	1.0	1.0	1.0	6	170	176	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7666, aminoacid position 2467	stopgain supported by majority of fwd and rev reads
+55	NC_045512.2	7780	3	stopgain	ORF1ab	11	6	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	11	1.0	1.0	1.0	6	5	11	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7780, aminoacid position 2505	stopgain supported by majority of fwd and rev reads
+56	NC_045512.2	7783	3	stopgain	ORF1ab	11	6	5	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	11	1.0	1.0	1.0	6	5	11	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7783, aminoacid position 2506	stopgain supported by majority of fwd and rev reads
+57	NC_045512.2	7804	3	stopgain	ORF1ab	12	6	6	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	12	1.0	1.0	1.0	6	6	12	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7804, aminoacid position 2513	stopgain supported by majority of fwd and rev reads
+58	NC_045512.2	7831	3	stopgain	ORF1ab	12	6	6	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	12	1.0	1.0	1.0	6	6	12	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7831, aminoacid position 2522	stopgain supported by majority of fwd and rev reads
+59	NC_045512.2	7852	3	stopgain	ORF1ab	12	6	6	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	12	1.0	1.0	1.0	6	6	12	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7852, aminoacid position 2529	stopgain supported by majority of fwd and rev reads
+60	NC_045512.2	7855	3	stopgain	ORF1ab	12	6	6	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	12	1.0	1.0	1.0	6	6	12	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7855, aminoacid position 2530	stopgain supported by majority of fwd and rev reads
+61	NC_045512.2	7861	3	stopgain	ORF1ab	11	5	6	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	11	1.0	1.0	1.0	5	6	11	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7861, aminoacid position 2532	stopgain supported by majority of fwd and rev reads
+62	NC_045512.2	7999	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 7999, aminoacid position 2578	only fwd or rev reads available, stopgain supported by the majority of them
+63	NC_045512.2	8008	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8008, aminoacid position 2581	only fwd or rev reads available, stopgain supported by the majority of them
+64	NC_045512.2	8011	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8011, aminoacid position 2582	only fwd or rev reads available, stopgain supported by the majority of them
+65	NC_045512.2	8029	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8029, aminoacid position 2588	only fwd or rev reads available, stopgain supported by the majority of them
+66	NC_045512.2	8038	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8038, aminoacid position 2591	only fwd or rev reads available, stopgain supported by the majority of them
+67	NC_045512.2	8050	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8050, aminoacid position 2595	only fwd or rev reads available, stopgain supported by the majority of them
+68	NC_045512.2	8071	3	stopgain	ORF1ab	23	23	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	23	1.0	1.0	0	23	0	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8071, aminoacid position 2602	only fwd or rev reads available, stopgain supported by the majority of them
+69	NC_045512.2	8119	3	stopgain	ORF1ab	46	23	23	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	46	1.0	1.0	1.0	23	23	46	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8119, aminoacid position 2618	stopgain supported by majority of fwd and rev reads
+70	NC_045512.2	8191	3	stopgain	ORF1ab	42	19	23	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	42	1.0	1.0	1.0	19	23	42	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8191, aminoacid position 2642	stopgain supported by majority of fwd and rev reads
+71	NC_045512.2	8209	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8209, aminoacid position 2648	only fwd or rev reads available, stopgain supported by the majority of them
+72	NC_045512.2	8221	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8221, aminoacid position 2652	only fwd or rev reads available, stopgain supported by the majority of them
+73	NC_045512.2	8230	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8230, aminoacid position 2655	only fwd or rev reads available, stopgain supported by the majority of them
+74	NC_045512.2	8248	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8248, aminoacid position 2661	only fwd or rev reads available, stopgain supported by the majority of them
+75	NC_045512.2	8269	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8269, aminoacid position 2668	only fwd or rev reads available, stopgain supported by the majority of them
+76	NC_045512.2	8275	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8275, aminoacid position 2670	only fwd or rev reads available, stopgain supported by the majority of them
+77	NC_045512.2	8278	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8278, aminoacid position 2671	only fwd or rev reads available, stopgain supported by the majority of them
+78	NC_045512.2	8296	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8296, aminoacid position 2677	only fwd or rev reads available, stopgain supported by the majority of them
+79	NC_045512.2	8305	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	23	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8305, aminoacid position 2680	only fwd or rev reads available, stopgain supported by the majority of them
+80	NC_045512.2	8656	3	stopgain	ORF1ab	10	10	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	10	1.0	1.0	0	10	0	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8656, aminoacid position 2797	only fwd or rev reads available, stopgain supported by the majority of them
+81	NC_045512.2	8665	3	stopgain	ORF1ab	10	10	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	10	1.0	1.0	0	10	0	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8665, aminoacid position 2800	only fwd or rev reads available, stopgain supported by the majority of them
+82	NC_045512.2	8677	3	stopgain	ORF1ab	10	10	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	10	1.0	1.0	0	10	0	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8677, aminoacid position 2804	only fwd or rev reads available, stopgain supported by the majority of them
+83	NC_045512.2	8701	3	stopgain	ORF1ab	10	10	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	10	1.0	1.0	0	10	0	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8701, aminoacid position 2812	only fwd or rev reads available, stopgain supported by the majority of them
+84	NC_045512.2	8719	3	stopgain	ORF1ab	10	10	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	10	1.0	1.0	0	10	0	10	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 8719, aminoacid position 2818	only fwd or rev reads available, stopgain supported by the majority of them
+85	NC_045512.2	8740	1	deletion	ORF1ab	20	10	10	10	0.5	0.5	0.5	5	5	0	0.0	0.0	0.0	0	0	0	0	0	0	0	0	10	[21101]	[5600, 5601, 18800]	1	b'T'	NC_045512.2	Gap of 1 nucleotide(s) found at refpos 8740	deletion supported by minority of fwd or rev reads [5%-50%]; homopolymeric; neighboring indels may restore reading frame
+86	NC_045512.2	9791	3	stopgain	ORF1ab	23	0	23	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	23	1.0	0	1.0	0	23	0	[]	[]	0	b'G'	NC_045512.2	Early Stopgain found at refpos 9791, aminoacid position 3175, with 1 mismatches	only fwd or rev reads available, stopgain supported by the majority of them
+87	NC_045512.2	18800	1	deletion	ORF1ab	111	54	57	66	0.5945945945945946	0.5925925925925926	0.5964912280701754	32	34	0	0.0	0.0	0.0	0	0	0	0	0	0	0	0	45	[21101]	[5600, 5601, 8740]	1	b'A'	NC_045512.2	Gap of 1 nucleotide(s) found at refpos 18800	deletion supported by majority of fwd and rev reads; homopolymeric; neighboring indels may restore reading frame
+88	NC_045512.2	18845	3	stopgain	ORF1ab	104	47	57	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	104	1.0	1.0	1.0	47	57	104	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 18845, aminoacid position 6193	stopgain supported by majority of fwd and rev reads
+89	NC_045512.2	18866	3	stopgain	ORF1ab	57	0	57	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	57	1.0	0	1.0	0	57	57	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 18866, aminoacid position 6200	only fwd or rev reads available, stopgain supported by the majority of them
+90	NC_045512.2	18878	3	stopgain	ORF1ab	57	0	57	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	57	1.0	0	1.0	0	57	57	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 18878, aminoacid position 6204	only fwd or rev reads available, stopgain supported by the majority of them
+91	NC_045512.2	18932	3	stopgain	ORF1ab	65	8	57	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	65	1.0	1.0	1.0	8	57	65	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 18932, aminoacid position 6222	stopgain supported by majority of fwd and rev reads
+92	NC_045512.2	18947	3	stopgain	ORF1ab	65	8	57	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	65	1.0	1.0	1.0	8	57	65	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 18947, aminoacid position 6227	stopgain supported by majority of fwd and rev reads
+93	NC_045512.2	19076	3	stopgain	ORF1ab	16	8	8	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	16	1.0	1.0	1.0	8	8	16	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19076, aminoacid position 6270	stopgain supported by majority of fwd and rev reads
+94	NC_045512.2	19127	3	stopgain	ORF1ab	16	8	8	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	16	1.0	1.0	1.0	8	8	16	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19127, aminoacid position 6287	stopgain supported by majority of fwd and rev reads
+95	NC_045512.2	19301	3	stopgain	ORF1ab	104	104	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	104	1.0	1.0	0	104	0	104	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19301, aminoacid position 6345	only fwd or rev reads available, stopgain supported by the majority of them
+96	NC_045512.2	19355	3	stopgain	ORF1ab	104	104	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	104	1.0	1.0	0	104	0	104	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19355, aminoacid position 6363	only fwd or rev reads available, stopgain supported by the majority of them
+97	NC_045512.2	19415	3	stopgain	ORF1ab	201	101	100	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	201	1.0	1.0	1.0	101	100	201	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19415, aminoacid position 6383	stopgain supported by majority of fwd and rev reads
+98	NC_045512.2	19427	3	stopgain	ORF1ab	200	100	100	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	200	1.0	1.0	1.0	100	100	200	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19427, aminoacid position 6387	stopgain supported by majority of fwd and rev reads
+99	NC_045512.2	19442	3	stopgain	ORF1ab	197	96	101	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	197	1.0	1.0	1.0	96	101	197	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19442, aminoacid position 6392	stopgain supported by majority of fwd and rev reads
+100	NC_045512.2	19460	3	stopgain	ORF1ab	108	7	101	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	108	1.0	1.0	1.0	7	101	108	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19460, aminoacid position 6398	stopgain supported by majority of fwd and rev reads
+101	NC_045512.2	19475	3	stopgain	ORF1ab	103	0	103	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	103	1.0	0	1.0	0	103	103	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19475, aminoacid position 6403	only fwd or rev reads available, stopgain supported by the majority of them
+102	NC_045512.2	19538	3	stopgain	ORF1ab	103	0	103	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	103	1.0	0	1.0	0	103	103	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19538, aminoacid position 6424	only fwd or rev reads available, stopgain supported by the majority of them
+103	NC_045512.2	19541	3	stopgain	ORF1ab	103	0	103	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	103	1.0	0	1.0	0	103	103	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19541, aminoacid position 6425	only fwd or rev reads available, stopgain supported by the majority of them
+104	NC_045512.2	19625	3	stopgain	ORF1ab	39	39	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	39	1.0	1.0	0	39	0	39	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19625, aminoacid position 6453	only fwd or rev reads available, stopgain supported by the majority of them
+105	NC_045512.2	19649	3	stopgain	ORF1ab	40	39	1	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	40	1.0	1.0	1.0	39	1	40	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19649, aminoacid position 6461	stopgain supported by majority of fwd and rev reads
+106	NC_045512.2	19739	3	stopgain	ORF1ab	78	39	39	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	78	1.0	1.0	1.0	39	39	78	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19739, aminoacid position 6491	stopgain supported by majority of fwd and rev reads
+107	NC_045512.2	19778	3	stopgain	ORF1ab	77	38	39	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	77	1.0	1.0	1.0	38	39	77	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19778, aminoacid position 6504	stopgain supported by majority of fwd and rev reads
+108	NC_045512.2	19826	3	stopgain	ORF1ab	39	0	39	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	39	1.0	0	1.0	0	39	39	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19826, aminoacid position 6520	only fwd or rev reads available, stopgain supported by the majority of them
+109	NC_045512.2	19871	3	stopgain	ORF1ab	108	69	39	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	108	1.0	1.0	1.0	69	39	108	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19871, aminoacid position 6535	stopgain supported by majority of fwd and rev reads
+110	NC_045512.2	19931	3	stopgain	ORF1ab	69	69	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	69	1.0	1.0	0	69	0	69	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19931, aminoacid position 6555	only fwd or rev reads available, stopgain supported by the majority of them
+111	NC_045512.2	19940	3	stopgain	ORF1ab	69	69	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	68	0.9855072463768116	0.9855072463768116	0	68	0	68	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 19940, aminoacid position 6558	only fwd or rev reads available, stopgain supported by the majority of them
+112	NC_045512.2	20012	3	stopgain	ORF1ab	131	69	62	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	131	1.0	1.0	1.0	69	62	131	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20012, aminoacid position 6582	stopgain supported by majority of fwd and rev reads
+113	NC_045512.2	20084	3	stopgain	ORF1ab	133	64	69	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	133	1.0	1.0	1.0	64	69	133	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20084, aminoacid position 6606	stopgain supported by majority of fwd and rev reads
+114	NC_045512.2	20120	3	stopgain	ORF1ab	69	0	69	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	69	1.0	0	1.0	0	69	69	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20120, aminoacid position 6618	only fwd or rev reads available, stopgain supported by the majority of them
+115	NC_045512.2	20135	3	stopgain	ORF1ab	69	0	69	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	69	1.0	0	1.0	0	69	69	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20135, aminoacid position 6623	only fwd or rev reads available, stopgain supported by the majority of them
+116	NC_045512.2	20534	3	stopgain	ORF1ab	251	251	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	251	1.0	1.0	0	251	0	251	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20534, aminoacid position 6756	only fwd or rev reads available, stopgain supported by the majority of them
+117	NC_045512.2	20537	3	stopgain	ORF1ab	251	251	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	251	1.0	1.0	0	251	0	251	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20537, aminoacid position 6757	only fwd or rev reads available, stopgain supported by the majority of them
+118	NC_045512.2	20558	3	stopgain	ORF1ab	250	250	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	250	1.0	1.0	0	250	0	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20558, aminoacid position 6764	only fwd or rev reads available, stopgain supported by the majority of them
+119	NC_045512.2	20579	3	stopgain	ORF1ab	250	250	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	250	1.0	1.0	0	250	0	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20579, aminoacid position 6771	only fwd or rev reads available, stopgain supported by the majority of them
+120	NC_045512.2	20633	3	stopgain	ORF1ab	250	249	1	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	250	1.0	1.0	1.0	249	1	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20633, aminoacid position 6789	stopgain supported by majority of fwd and rev reads
+121	NC_045512.2	20723	3	stopgain	ORF1ab	442	194	248	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	442	1.0	1.0	1.0	194	248	442	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20723, aminoacid position 6819	stopgain supported by majority of fwd and rev reads
+122	NC_045512.2	20777	3	stopgain	ORF1ab	250	0	250	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	250	1.0	0	1.0	0	250	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20777, aminoacid position 6837	only fwd or rev reads available, stopgain supported by the majority of them
+123	NC_045512.2	20780	3	stopgain	ORF1ab	250	0	250	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	250	1.0	0	1.0	0	250	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20780, aminoacid position 6838	only fwd or rev reads available, stopgain supported by the majority of them
+124	NC_045512.2	20783	3	stopgain	ORF1ab	250	0	250	0	0.0	0	0.0	0	0	0	0.0	0	0.0	0	0	250	1.0	0	1.0	0	250	250	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20783, aminoacid position 6839	only fwd or rev reads available, stopgain supported by the majority of them
+125	NC_045512.2	20819	3	stopgain	ORF1ab	275	24	251	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	275	1.0	1.0	1.0	24	251	275	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20819, aminoacid position 6851	stopgain supported by majority of fwd and rev reads
+126	NC_045512.2	20828	3	stopgain	ORF1ab	275	24	251	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	274	0.9963636363636363	1.0	0.9960159362549801	24	250	274	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20828, aminoacid position 6854	stopgain supported by majority of fwd and rev reads
+127	NC_045512.2	20834	3	stopgain	ORF1ab	275	24	251	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	275	1.0	1.0	1.0	24	251	275	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20834, aminoacid position 6856	stopgain supported by majority of fwd and rev reads
+128	NC_045512.2	20852	3	stopgain	ORF1ab	275	24	251	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	275	1.0	1.0	1.0	24	251	275	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20852, aminoacid position 6862	stopgain supported by majority of fwd and rev reads
+129	NC_045512.2	20912	3	stopgain	ORF1ab	24	24	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	24	1.0	1.0	0	24	0	24	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20912, aminoacid position 6882	only fwd or rev reads available, stopgain supported by the majority of them
+130	NC_045512.2	20990	3	stopgain	ORF1ab	48	24	24	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	48	1.0	1.0	1.0	24	24	48	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 20990, aminoacid position 6908	stopgain supported by majority of fwd and rev reads
+131	NC_045512.2	21140	3	stopgain	ORF1ab	41	17	24	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	41	1.0	1.0	1.0	17	24	41	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21140, aminoacid position 6958	stopgain supported by majority of fwd and rev reads
+132	NC_045512.2	21164	3	stopgain	ORF1ab	17	17	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	17	1.0	1.0	0	17	0	17	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21164, aminoacid position 6966	only fwd or rev reads available, stopgain supported by the majority of them
+133	NC_045512.2	21170	3	stopgain	ORF1ab	17	17	0	0	0.0	0.0	0	0	0	0	0.0	0.0	0	0	0	17	1.0	1.0	0	17	0	17	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21170, aminoacid position 6968	only fwd or rev reads available, stopgain supported by the majority of them
+134	NC_045512.2	21248	3	stopgain	ORF1ab	34	17	17	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	34	1.0	1.0	1.0	17	17	34	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21248, aminoacid position 6994	stopgain supported by majority of fwd and rev reads
+135	NC_045512.2	21275	3	stopgain	ORF1ab	34	17	17	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	34	1.0	1.0	1.0	17	17	34	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21275, aminoacid position 7003	stopgain supported by majority of fwd and rev reads
+136	NC_045512.2	21314	3	stopgain	ORF1ab	31	14	17	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	31	1.0	1.0	1.0	14	17	31	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21314, aminoacid position 7016	stopgain supported by majority of fwd and rev reads
+137	NC_045512.2	21398	3	stopgain	ORF1ab	21	4	17	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	21	1.0	1.0	1.0	4	17	21	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21398, aminoacid position 7044	stopgain supported by majority of fwd and rev reads
+138	NC_045512.2	21419	3	stopgain	ORF1ab	21	4	17	0	0.0	0.0	0.0	0	0	0	0.0	0.0	0.0	0	0	21	1.0	1.0	1.0	4	17	21	[]	[]	0	b'T'	NC_045512.2	Early Stopgain found at refpos 21419, aminoacid position 7051	stopgain supported by majority of fwd and rev reads