Mapping of reads to selected viruses in DAMIAN results

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Tags: pipeline

  1. Prepare input raw data

    # -- Ringversuch --
~/DATA/Data_Damian/241213_VH00358_120_AAG523FM5_Ringversuch
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R1_001.fastq.gz RV1_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R2_001.fastq.gz RV1_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R1_001.fastq.gz RV2_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R2_001.fastq.gz RV2_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R1_001.fastq.gz RV3_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R2_001.fastq.gz RV3_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R1_001.fastq.gz RV4_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R2_001.fastq.gz RV4_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R1_001.fastq.gz RV5_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R2_001.fastq.gz RV5_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R1_001.fastq.gz RV6_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R2_001.fastq.gz RV6_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R1_001.fastq.gz RV1_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R2_001.fastq.gz RV1_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R1_001.fastq.gz RV2_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R2_001.fastq.gz RV2_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R1_001.fastq.gz RV3_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R2_001.fastq.gz RV3_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R1_001.fastq.gz RV4_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R2_001.fastq.gz RV4_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R1_001.fastq.gz RV5_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R2_001.fastq.gz RV5_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R1_001.fastq.gz RV6_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R2_001.fastq.gz RV6_RNA_R2.fastq.gz

  2. Prepare virus database and select 8 representatives for the eight given viruses from the database

    # -- Download all genomes --
# enterovirus D68
# HSV-1
# HSV-2
# Influenza A H1N1
# Cytomegalovirus AD169 (The genome size of Human herpesvirus 5 (HHV-5) — more commonly known as Cytomegalovirus (CMV))
# Influenza A H3N2
# Monkeypox
# HIV-1

esearch -db nucleotide -query "txid42789[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_42789_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_42789_ncbi.fasta complete_42789_ncbi.fasta    #899
esearch -db nucleotide -query "txid10298[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10298_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10298_ncbi.fasta complete_10298_ncbi.fasta    #162
esearch -db nucleotide -query "txid10310[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10310_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10310_ncbi.fasta complete_10310_ncbi.fasta    #33
esearch -db nucleotide -query "txid1323429[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_1323429_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_1323429_ncbi.fasta complete_1323429_ncbi.fasta    #465
esearch -db nucleotide -query "txid10360[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10360_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_10360_ncbi.fasta complete_10360_ncbi.fasta    #1
esearch -db nucleotide -query "txid41857[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_41857_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_41857_ncbi.fasta complete_41857_ncbi.fasta    #120
esearch -db nucleotide -query "txid10244[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10244_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10244_ncbi.fasta complete_10244_ncbi.fasta    #2525
esearch -db nucleotide -query "txid11676[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_11676_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_11676_ncbi.fasta complete_11676_ncbi.fasta    #485995-->7416

# ---- Alternatively, using ENA instead to download the genomes ----
# https://www.ebi.ac.uk/ena/browser/view/11676 (1138065 records)
# #Click "Sequence" and download "Counts" (1132648) and "Taxon descendants count" (1138065) if there is enough time! Downloading time points is 09.04.2025.
# python ~/Scripts/filter_fasta.py  ena_11676_sequence.fasta complete_11676_ena.fasta  #1138065-->????

# Virus Name    NCBI TaxID
# ------------------------
# Enterovirus D68   42789                             >PQ895337.1 Enterovirus D68 isolate SH2024-25870
# HSV-1 (Herpes Simplex Virus 1)    10298             >PQ569920.1 Human alphaherpesvirus 1 isolate MacIntyre, complete genome
# HSV-2 (Herpes Simplex Virus 2)    10310             >OM370995.1 Human alphaherpesvirus 2 strain G, complete genome

    samtools faidx complete_42789_ncbi.fasta PQ895337.1 > Enterovirus_D68_isolate_SH2024-25870.fasta
    samtools faidx complete_10298_ncbi.fasta PQ569920.1 > HSV-1_isolate_MacIntyre.fasta
    samtools faidx complete_10310_ncbi.fasta OM370995.1 > HSV-2_strain_G.fasta

# Influenza A virus (H1N1)  1323429
# The Influenza A virus (H1N1) genome is composed of eight single-stranded negative-sense RNA segments, and the total genome size is approximately 13,500 nucleotides (13.5 kb).
# Segment   Gene    Protein Product(s)  Approx. Length (nt)
# 1 PB2 Polymerase basic 2  ~2,341
# 2 PB1 Polymerase basic 1, PB1-F2  ~2,341
# 3 PA  Polymerase acidic   ~2,233
# 4 HA  Hemagglutinin   ~1,778
# 5 NP  Nucleoprotein   ~1,565
# 6 NA  Neuraminidase   ~1,413
# 7 M   Matrix proteins (M1, M2)    ~1,027
# 8 NS  Nonstructural (NS1, NS2)    ~890

# >LC662544.1 Influenza A virus (H1N1) A/PR/8/34 NEP, NS1 genes for nonstructural protein 2, nonstructural protein 1, complete cds
# >LC662543.1 Influenza A virus (H1N1) A/PR/8/34 M2, M1 genes for matrix protein 2, matrix protein 1, complete cds
# >LC662542.1 Influenza A virus (H1N1) A/PR/8/34 NA gene for neuraminidase, complete cds
# >LC662541.1 Influenza A virus (H1N1) A/PR/8/34 NP gene for nucleoprotein, complete cds
# >LC662540.1 Influenza A virus (H1N1) A/PR/8/34 HA gene for haemagglutinin, complete cds
# >LC662539.1 Influenza A virus (H1N1) A/PR/8/34 PA, PA-X genes for polymerase PA, PA-X protein, complete cds
# >LC662538.1 Influenza A virus (H1N1) A/PR/8/34 PB1, PB1-F2 genes for polymerase PB1, PB1-F2 protein, complete cds
# >LC662537.1 Influenza A virus (H1N1) A/PR/8/34 PB2 gene for polymerase PB2, complete cds

    samtools faidx complete_1323429_ncbi.fasta LC662537.1 > H1N1_A-PR-8-34_PB2.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662538.1 > H1N1_A-PR-8-34_PB1.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662539.1 > H1N1_A-PR-8-34_PA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662540.1 > H1N1_A-PR-8-34_HA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662541.1 > H1N1_A-PR-8-34_NP.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662542.1 > H1N1_A-PR-8-34_NA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662543.1 > H1N1_A-PR-8-34_M.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662544.1 > H1N1_A-PR-8-34_NS.fasta

# Human cytomegalovirus AD169   10360

# Influenza A virus (H3N2)  41857

# >LC817411.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 8, complete sequence
# >LC817410.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 7, complete sequence
# >LC817409.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 6, complete sequence
# >LC817408.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 5, complete sequence
# >LC817407.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 4, complete sequence
# >LC817406.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 3, complete sequence
# >LC817405.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 2, complete sequence
# >LC817404.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 1, complete sequence

    samtools faidx complete_41857_ncbi.fasta LC817404.1 > H3N2_A-Fukushima-OR808-2023_PB2.fasta
    samtools faidx complete_41857_ncbi.fasta LC817405.1 > H3N2_A-Fukushima-OR808-2023_PB1.fasta
    samtools faidx complete_41857_ncbi.fasta LC817406.1 > H3N2_A-Fukushima-OR808-2023_PA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817407.1 > H3N2_A-Fukushima-OR808-2023_HA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817408.1 > H3N2_A-Fukushima-OR808-2023_NP.fasta
    samtools faidx complete_41857_ncbi.fasta LC817409.1 > H3N2_A-Fukushima-OR808-2023_NA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817410.1 > H3N2_A-Fukushima-OR808-2023_M.fasta
    samtools faidx complete_41857_ncbi.fasta LC817411.1 > H3N2_A-Fukushima-OR808-2023_NS.fasta

# Monkeypox virus   10244: >OP689666.1 Monkeypox virus isolate MPXV/Germany/2022/RKI513, complete genome
    samtools faidx complete_10244_ncbi.fasta OP689666.1 > Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta

# Human immunodeficiency virus 1    11676: >AJ866558.1 Human immunodeficiency virus 1 complete genome, isolate 01IC-PCI127
    samtools faidx complete_11676_ncbi.fasta AJ866558.1 >  HIV-1_isolate_01IC-PCI127.fasta

# -- Selected genomes saved in the fasta-files --
# Enterovirus_D68_isolate_SH2024-25870.fasta
# HSV-1_isolate_MacIntyre.fasta
# HSV-2_strain_G.fasta
# H1N1_A-PR-8-34_PB2.fasta
# H1N1_A-PR-8-34_PB1.fasta
# H1N1_A-PR-8-34_PA.fasta
# H1N1_A-PR-8-34_HA.fasta
# H1N1_A-PR-8-34_NP.fasta
# H1N1_A-PR-8-34_NA.fasta
# H1N1_A-PR-8-34_M.fasta
# H1N1_A-PR-8-34_NS.fasta
# Human_cytomegalovirus_strain_AD169.fasta
# H3N2_A-Fukushima-OR808-2023_PB2.fasta
# H3N2_A-Fukushima-OR808-2023_PB1.fasta
# H3N2_A-Fukushima-OR808-2023_PA.fasta
# H3N2_A-Fukushima-OR808-2023_HA.fasta
# H3N2_A-Fukushima-OR808-2023_NP.fasta
# H3N2_A-Fukushima-OR808-2023_NA.fasta
# H3N2_A-Fukushima-OR808-2023_M.fasta
# H3N2_A-Fukushima-OR808-2023_NS.fasta
# Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta
# HIV-1_isolate_01IC-PCI127.fasta

  3. (Optional) Run the first round of vrap (--virus==viruses_selected.fasta)

    ln -s ~/Tools/vrap/ .
mamba activate /home/jhuang/miniconda3/envs/vrap

cd ~/DATA/Data_Damian/vrap_Ringversuch
cat complete_10244_ncbi.fasta complete_10298_ncbi.fasta complete_10310_ncbi.fasta complete_1323429_ncbi.fasta complete_10360_ncbi.fasta complete_41857_ncbi.fasta complete_10244_ncbi.fasta complete_11676_ncbi.fasta > viruses_selected.fasta

#Run vrap (first round): replace --virus to the specific taxonomy (e.g. viruses_selected.fasta) --> change virus_user_db --> specific_bacteria_user_db
(vrap) for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    vrap/vrap.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample} --bt2idx=/home/jhuang/REFs/genome --host=/home/jhuang/REFs/genome.fa --virus=/home/jhuang/DATA/Data_Damian/vrap_Ringversuch/viruses_selected.fasta --nt=/mnt/nvme1n1p1/blast/nt --nr=/mnt/nvme1n1p1/blast/nr  -t 100 -l 200  -g
done

  4. Run the second round of vrap (--host==${virus}.fasta)

    cat Enterovirus_D68_isolate_SH2024-25870.fasta HSV-1_isolate_MacIntyre.fasta HSV-2_strain_G.fasta H1N1_A-PR-8-34_PB2.fasta H1N1_A-PR-8-34_PB1.fasta H1N1_A-PR-8-34_PA.fasta H1N1_A-PR-8-34_HA.fasta H1N1_A-PR-8-34_NP.fasta H1N1_A-PR-8-34_NA.fasta H1N1_A-PR-8-34_M.fasta H1N1_A-PR-8-34_NS.fasta Human_cytomegalovirus_strain_AD169.fasta H3N2_A-Fukushima-OR808-2023_PB2.fasta H3N2_A-Fukushima-OR808-2023_PB1.fasta H3N2_A-Fukushima-OR808-2023_PA.fasta H3N2_A-Fukushima-OR808-2023_HA.fasta H3N2_A-Fukushima-OR808-2023_NP.fasta H3N2_A-Fukushima-OR808-2023_NA.fasta H3N2_A-Fukushima-OR808-2023_M.fasta H3N2_A-Fukushima-OR808-2023_NS.fasta Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta HIV-1_isolate_01IC-PCI127.fasta > viruses_representative.fasta

# Run vrap (second round): selecte some representative viruses from the generated Excel-files generated by the last step as --host
(vrap) for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    vrap/vrap_until_bowtie2.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample}_on_representatives --host /home/jhuang/DATA/Data_Damian/vrap_Ringversuch/viruses_representative.fasta   -t 100 -l 200  --gbt2 --noblast
done

  5. Generate the mapping statistics for the sam-files generated from last step

    for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    echo "-----${sample}_on_representatives------" >> LOG_mapping
    #cd vrap_${sample}_on_${virus}/bowtie
    cd vrap_${sample}_on_representatives/bowtie
    # Rename and convert SAM to BAM
    mv mapped mapped.sam 2>> ../../LOG_mapping
    samtools view -S -b mapped.sam > mapped.bam 2>> ../../LOG_mapping
    samtools sort mapped.bam -o mapped_sorted.bam 2>> ../../LOG_mapping
    samtools index mapped_sorted.bam 2>> ../../LOG_mapping
    # Write flagstat output to log (go up two levels to write correctly)
    samtools flagstat mapped_sorted.bam >> ../../LOG_mapping 2>&1
    cd ../..
done

#draw some plots for some representative isolates which found in the first round (see Excel-file).
samtools depth -m 0 -a mapped_sorted.bam > coverage.txt
grep "PQ895337.1" coverage.txt > PQ895337_coverage.txt
grep "PQ569920.1" coverage.txt > PQ569920_coverage.txt

        import pandas as pd
        import matplotlib.pyplot as plt

        # Load coverage data
        df = pd.read_csv("PQ895337_coverage.txt", sep="\t", header=None, names=["chr", "pos", "coverage"])

        # Plot
        plt.figure(figsize=(10,4))
        plt.plot(df["pos"], df["coverage"], color="blue", linewidth=0.5)
        plt.xlabel("Genomic Position")
        plt.ylabel("Coverage Depth")
        plt.title("BAM Coverage Plot")
        plt.show()

  6. Report

    Subject: Mapping Results and Selected Reference Genomes

Dear XXXX,

Please find below the results. For each of the viruses you sent me, a representative isolate has been selected, as listed below:

Selected Reference Isolates:

    Enterovirus D68:
        PQ895337.1 – Enterovirus D68 isolate SH2024-25870

    HSV-1 (Herpes Simplex Virus 1):
        PQ569920.1 – Human alphaherpesvirus 1 isolate MacIntyre, complete genome

    HSV-2 (Herpes Simplex Virus 2):
        OM370995.1 – Human alphaherpesvirus 2 strain G, complete genome

    Influenza A virus (H1N1):

        LC662537.1 – Influenza A virus (H1N1) A/PR/8/34 PB2 gene for polymerase PB2, complete cds
        LC662538.1 – Influenza A virus (H1N1) A/PR/8/34 PB1, PB1-F2 genes for polymerase PB1, PB1-F2 protein, complete cds
        LC662539.1 – Influenza A virus (H1N1) A/PR/8/34 PA, PA-X genes for polymerase PA, PA-X protein, complete cds
        LC662540.1 – Influenza A virus (H1N1) A/PR/8/34 HA gene for haemagglutinin, complete cds
        LC662541.1 – Influenza A virus (H1N1) A/PR/8/34 NP gene for nucleoprotein, complete cds
        LC662542.1 – Influenza A virus (H1N1) A/PR/8/34 NA gene for neuraminidase, complete cds
        LC662543.1 – Influenza A virus (H1N1) A/PR/8/34 M2, M1 genes for matrix protein 2, matrix protein 1, complete cds
        LC662544.1 – Influenza A virus (H1N1) A/PR/8/34 NEP, NS1 genes for nonstructural protein 2, nonstructural protein 1, complete cds

    Cytomegalovirus (strain AD169):
        X17403.1 – Human cytomegalovirus strain AD169, complete genome

    Influenza A virus (H3N2):

        LC817404.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 PB2 gene, complete sequence
        LC817405.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 PB1 gene, complete sequence
        LC817406.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 PA gene, complete sequence
        LC817407.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 HA gene, complete sequence
        LC817408.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 NP gene, complete sequence
        LC817409.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 NA gene, complete sequence
        LC817410.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 M gene, complete sequence
        LC817411.1 – Influenza A virus H3N2 A_Fukushima_OR808_2023 NS gene, complete sequence

    Monkeypox virus:
        OP689666.1 – Isolate MPXV/Germany/2022/RKI513, complete genome

    Human Immunodeficiency Virus 1 (HIV-1):
        AJ866558.1 – Isolate 01IC-PCI127, complete genome

Mapping Results:

Then, we mapped the paired-end reads from 12 samples of the Ringversuch project against the reference genomes listed above. The following are the mapping statistics. Coverage plots are attached for each case where reads map to the reference genome (see attachments).

Mapping statistics:

    RV1_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV2_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV3_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV4_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV5_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV6_DNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV1_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV2_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV3_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV4_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV5_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)
    RV6_RNA_on_Enterovirus_D68_isolate_SH2024-25870: 0 + 0 mapped (0.00% : N/A)

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