1 GMS-Artic pipeline

1.1 Quality Checks
1.2 Alignment Statistics
1.3 Lineage analysis
1.4 VCF
1.5 Depth plot
1.6 Tools used and versions

1 GMS-Artic pipeline

The GMS-Artic aims to develop a nationwide standard open-source bioinformatic workflow to investigate SARS-CoV-2 whole genome sequencing for real-time clinical practices on the National Genomic Platform (NGP). A parallel work using the GMS-Artic framework designed to update all metadata information from the clinics and upload the output result to the Swedish Health Agency routinely. Continuous support on the pipeline development and an additional process like variant visualization is currently in progress.
The following analysis result is generated using the GMS-Artic v2.0.0. For details, please visit GitHub repo.

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	Description	Value
1	Length of illumina reads to keep after primer trimming	50
2	Sliding window quality threshold for keeping reads after primer trimming (illumina)	20
3	Mpileup depth for ivar (although undocumented in mpileup; setting to zero removes limit)	100000
4	iVar frequency threshold for consensus variant (ivar consensus: -t)	0.75
5	Minimum coverage depth to call variant (ivar consensus: -m; ivar variants -m)	10
6	iVar frequency threshold to call variant (ivar variants: -t )	0.25
7	iVar minimum mapQ to call variant (ivar variants: -q)	20
8	Typing frequency threshold to call aa consequences of variant. Set to ivarFreqThreshold for consistency with consensus	0.75
9	Minimum coverage depth to call aa consequences of variant. Set to ivarMinDepth for consistency with consensus	10

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*Description

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Sample_Name	qc_status	qc_notes	qc_overall_score	qc_overall_status
subsample4	pass	Ambiguous_content:0.02	1.694444	good
subsample2	pass	Ambiguous_content:0.13	159.22701	bad
subsample1	fail	Ambiguous_content:0.9	9578.884444	bad
subsample3	pass	Ambiguous_content:0.02	11.111111	good

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1.2 Alignment Statistics

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	Sample Name	Alignment Score	Alignment End	Frameshifts	Substitutions	Deletions	Insertions	AA_Substitutions	AA_Deletions
1	subsample4	89196	29903		C44T C241T T670G C1627T C2790T C3037T G4184A C4321T C9344T A9424G C9534T C10029T C10198T G10447A C10449A G12160A C12880T C14408T C15714T C17410T C17550T C17747T A17841G A18163G C19955T A20055G C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G T22917G G22992A C22995A A23013C T23018G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A C25000T C25584T C26060T A26086G C26270T G26529A C26549T C26577G G26709A A27038G C27807T C27889T A28271T C28311T A28330G G28361T G28371T G28881A G28882A G28883C A29510C	11288-11296 21633-21641 21765-21770 28362-28370 29734-29759		E:T9I M:D3N M:Q19E M:A63T N:P13L N:S33F N:R203K N:G204R N:S413R ORF1a:S135R ORF1a:T842I ORF1a:G1307S ORF1a:L3027F ORF1a:T3090I ORF1a:T3255I ORF1a:P3395H ORF1b:P314L ORF1b:R1315C ORF1b:P1427L ORF1b:I1566V ORF1b:T2163I ORF3a:T223I ORF3a:I232V ORF9b:P10S ORF9b:D16G ORF9b:A29I ORF9b:V30L S:T19I S:A27S S:G142D S:V213G S:G339D S:S371F S:S373P S:S375F S:T376A S:D405N S:R408S S:K417N S:N440K S:L452R S:S477N S:T478K S:E484A S:F486V S:Q498R S:N501Y S:Y505H S:D614G S:H655Y S:N679K S:P681H S:N764K S:D796Y S:Q954H S:N969K	N:G30- N:E31- N:R32- ORF1a:S3675- ORF1a:G3676- ORF1a:F3677- ORF9b:M26- ORF9b:E27- ORF9b:N28- S:L24- S:P25- S:P26- S:H69- S:V70-
2	subsample2	89705	29903		G26144T			ORF3a:G251V
3	subsample1	89702	29903	ORF6:38-62			27312:A
4	subsample3	89441	29903		G210T C241T T961C C1420T C3037T T3960C G4181T A6208G C6402T G6622A C7124T C8986T G9053T C10029T A11201G A11332G A12967G C14408T G14511C G15451A C16466T G16710T G18255T C19220T C21057T C21618G G21796T C21846T G21987A T22917G C22995A A23403G C23604G G24410A C25469T T25518C G25538T C26054A G26172T T26767C C27590T T27638C C27689T C27752T C27874T G28378T A28461G G28881T G28916T G29402T G29742T G29751T	22029-22034 28248-28253 28271		M:I82T N:D63G N:R203M N:G215C N:D377Y ORF1a:I1232T ORF1a:A1306S ORF1a:P2046L ORF1a:P2287S ORF1a:V2930L ORF1a:T3255I ORF1a:T3646A ORF1b:P314L ORF1b:Q348H ORF1b:G662S ORF1b:P1000L ORF1b:M1596I ORF1b:A1918V ORF3a:S26L ORF3a:G49V ORF3a:T221K ORF3a:M260I ORF7a:A66V ORF7a:V82A ORF7a:P99L ORF7a:T120I ORF7b:T40I ORF9b:R32L ORF9b:T60A S:T19R S:R78S S:T95I S:G142D S:R158G S:L452R S:T478K S:D614G S:P681R S:D950N	ORF8:D119- ORF8:F120- S:E156- S:F157-

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1.3 Lineage analysis

1.3.1 NextClade and Pangolin Table
1.3.2 Scorpio Table

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	Sample.Name	Pangolin.lineage	Pangolin.version	NextClade.version
1	subsample4	BA.5.2.1	4.2	22B
2	subsample2	B	4.2	19A
3	subsample1	Unassigned	4.2	19A
4	subsample3	AY.127	4.2	21J

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Sample Name	scorpio_version	scorpio_call	scorpio_support	scorpio_conflict	scorpio_notes
subsample4	0.3.18	Omicron (BA.5-like)	0.97	0.02	scorpio call: Alt alleles 59; Ref alleles 1; Amb alleles 0; Oth alleles 1
subsample2	0.3.18
subsample1	0.3.18
subsample3	0.3.18	Delta (B.1.617.2-like)	1	0	scorpio call: Alt alleles 13; Ref alleles 0; Amb alleles 0; Oth alleles 0

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1.4 VCF

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Sample Name	CHROM	POS	ID	REF	ALT	QUAL
subsample4	MN908947.3	27317	.	A	AT,T	762.297
subsample2	MN908947.3	26144	.	G	T	1356.84
subsample1	MN908947.3	44	.	C	T	311.884
subsample3	MN908947.3	241	.	C	T	2597.72
subsample4	MN908947.3	670	.	T	G	310010
subsample2	MN908947.3	1627	.	C	T	484884
subsample1	MN908947.3	2790	.	C	T	16932.6
subsample3	MN908947.3	3037	.	C	T	102520
subsample4	MN908947.3	4184	.	G	A	114614
subsample2	MN908947.3	4321	.	C	T	87243

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1.5 Depth plot

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1.6 Tools used and versions

Link to NextFlow Run - Please NOTE: This will works local only - where the pipeline runs

1.6.1 Container tools: versions
1.6.2 NextFlow timeline

Details are provided below:

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	tools	versions
1	bcftools	1.10.2
2	bwa	0.7.17-r1188
3	fastqc	0.11.9
4	freebayes	1.3.5
5	gofasta	1.2.0
6	ivar	1.3.1
7	multiqc	1.11
8	nextclade	1.10.2
9	picard	2.25.2
10	python	3.7.12

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SARS-CoV-2 WGS Analysis Report

Jyotirmoy Das

14 februari, 2023

1 GMS-Artic pipeline

1.1 Quality Checks

1.2 Alignment Statistics

1.3 Lineage analysis

1.4 VCF

1.5 Depth plot

1.6 Tools used and versions