Typing

This table gives the influenza type and strain for each sample. Samples are first aligned to IRMA to generate a consensus of alignments, and then typed with Abricate using the INSaFLU database. Please see the table in the section below ('Typing details') for full Abricate results. These results are especially useful if typing results are discordant.

Sample Barcode Type Archetype
H3N2-strain-A-Wisconsin-15-2009-VR-1882DQ barcode95
A
H3N2
Swine-Flu-ATCC-VR-1683D barcode96
A
H1N1
VR-1469DQ barcode94
A
H1N1
VR-1811D-H3N2 barcode92
A
H3N2

Typing details

Sequence Gene Coverage Coverage Map Gaps %Coverage %Identity Details
A_HA_H3 HA 1-1701/1701 =============== 0/0 100.0 96.24 H3
A_MP M1 1-982/982 =============== 0/0 100.0 98.17 Type_A
A_NA_N2 nan 1-1410/1410 =============== 0/0 100.0 96.45 N2
Sequence Gene Coverage Coverage Map Gaps %Coverage %Identity Details
A_HA_H1 HA 1-1701/1701 ========/====== 1/1 100.0 82.67 H1
A_MP M1 1-982/982 =============== 0/0 100.0 89.82 Type_A
A_NA_N1 nan 1-1409/1410 ========/====== 3/6 99.72 84.14 N1
Sequence Gene Coverage Coverage Map Gaps %Coverage %Identity Details
A_HA_H1 HA 1-1699/1701 ========/====== 8/12 99.53 79.18 H1
A_MP M1 1-982/982 =============== 0/0 100.0 90.83 Type_A
A_NA_N1 nan 1-1409/1410 ========/====== 4/8 99.5 79.94 N1
Sequence Gene Coverage Coverage Map Gaps %Coverage %Identity Details
A_HA_H3 HA 1-1701/1701 ========/====== 1/3 100.0 95.78 H3
A_MP M1 1-982/982 =============== 0/0 100.0 91.45 Type_A
A_NA_N2 nan 1-1410/1410 =============== 0/0 100.0 96.17 N2

Select samples from the drop-down in this table to view detailed Abricate results.

Coverage

The heatmap shows the median coverage per segment for each sample. Each box in the heatmap represents one segment in a sample and is colour-coded using the range of values in the slider (from zero to maximum median coverage across the whole batch). The slider can be manipulated to filter the heatmap by coverage levels, enabling a quick assessment of the coverage for each sample.

Nextclade results

Sample Strain Gene Coverage Clade Warnings
Sample Strain Gene Coverage Clade Warnings
Swine-Flu-ATCC-VR-1683D H1N1 NA 0.98 A.1.1
VR-1469DQ H1N1 NA 0.97 A.1.1
Sample Strain Gene Coverage Clade Warnings
H3N2-strain-A-Wisconsin-15-2009-VR-1882DQ H3N2 HA 0.99 3C.3a
VR-1811D-H3N2 H3N2 HA 0.99 3C.3a
Sample Strain Gene Coverage Clade Warnings
VR-1811D-H3N2 H3N2 NA 0.98 unassigned
H3N2-strain-A-Wisconsin-15-2009-VR-1882DQ H3N2 NA 0.98 unassigned

Read summary

Software versions

Name Version
pysam 0.20.0
fastcat 0.10.2
bcftools 1.16
samtools 1.16.1
abricate 1.0.1

Workflow parameters

Key Value
analyse_unclassified False
fastq test_data/fastq
out_dir wf-flu
sample_sheet test_data/sample_sheet.csv
min_coverage 20
downsample 50
min_qscore 9
override_basecaller_cfg None
rbk False
store_dir wf-flu/store_dir
_reference /builds/kcaVU3FG/0/epi2melabs/workflows/wf-flu/./data/primer_schemes/V1/consensus_irma.fasta
_blastdb /builds/kcaVU3FG/0/epi2melabs/workflows/wf-flu/./data/primer_schemes/V1/blastdb