Genome Detective

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Analysis Results

Analysis of SRR22472796_SarsCoV2_amplicon_example

Technology

Paired-end short reads

Input Files

SRR22472796_SarsCoV2_amplicon_example_1.fastq.gz (13.39 MB), SRR22472796_SarsCoV2_amplicon_example_2.fastq.gz (15.12 MB)

Protocol

Default Virus Analysis (metagenome)

Submitted On

2022-12-02 13:08:33 UTC

Release Version

panviral2.43

Statistics

Original Read Length

35 - 151

Trimmed Read Length

50 - 136

	# Reads	% of Reads
Input file	392426	100.0%
After QC	330128	84.1%
After filtering	325826	83.0%
Mapped back to contigs	324739	82.8%

Quality Control (QC) reports

Before Preprocessing

After Preprocessing

Taxonomy chart Taxonomy tree

Include Discovery

Scaling

Assignments

Strains with at least 50% NT similarity (assuming a 45% similarity for non-covered parts)

Assignment

# Reads

Depth of Coverage

NT Identity

AA Identity

Genome Coverage

Genome Coverage image

Severe acute respiratory syndrome-related coronavirus (subtype: SARS-CoV-2, Omicron (BA.2 21L))

324739

1232.4

99.7%

99.6%

99.9%

Discoveries

Strains with low NT identity and/or low genome coverage

No strains found that meet the discovery requirements.

Download Assignment and Discovery table:

Download analysis files

Consensus Sequences

consensus sequences (assignment, discovery)

Consensus Contigs

consensus contigs (assignment, discovery)

Unused Reads

unused reads file not available for download

Unused Contigs

unused contigs file not available for download

Bam Files

BAM files