# HG changeset patch
# User iuc
# Date 1685553011 0
# Node ID f079716f598ce30fdc9f54e82405b3dfca633735
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities commit f6d1be0a6643389820c4622d4cb996ac03531107
diff -r 000000000000 -r f079716f598c frameshift_deletions_checks.xml
--- /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 @@
+
+ reports on frameshifting indels in consensus sequence
+
+ macros.xml
+
+
+
+ smallgenomeutilities
+
+
+
+ &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
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `_.
+
+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
+]]>
+
+
+
diff -r 000000000000 -r f079716f598c macros.xml
--- /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 @@
+
+ 0.3.9
+ 0
+ 21.09
+
+
+ v-pipe
+
+
+
+
+ 10.1093/bioinformatics/btab015
+
+
+
diff -r 000000000000 -r f079716f598c test-data/Genes_NC_045512.2.GFF3
--- /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
+###
diff -r 000000000000 -r f079716f598c test-data/NC_045512.2.fasta.gz
Binary file test-data/NC_045512.2.fasta.gz has changed
diff -r 000000000000 -r f079716f598c test-data/REF_aln_trim.cram
Binary file test-data/REF_aln_trim.cram has changed
diff -r 000000000000 -r f079716f598c test-data/REF_aln_trim.cram.crai
Binary file test-data/REF_aln_trim.cram.crai has changed
diff -r 000000000000 -r f079716f598c test-data/consensus.bcftools.fasta.gz
Binary file test-data/consensus.bcftools.fasta.gz has changed
diff -r 000000000000 -r f079716f598c test-data/frameshift_deletions_check.tsv
--- /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