Supplementary Materials for Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China Adrian Jones, Daoyu Zhang, Steven E. Massey, Yuri Deigin, Louis R. Nemzer, Steven C. Quay Supplementary Information Supp_Info_1.xlsx: BioProject PRJNA602160 SRA analysis. Supp_Info_2.xlsx: Mitochondrial sequence analysis for all SRA datasets in BioProject PRJNA602160. Supp_Info_3.xlsx: MERS-CoV sequence analysis from SRA datasets in BioProject PRJNA602160. Supp_Infor_4.xlsx: Analysis results for control datasets in PRJNA602115. Supplementary Data Snapgene annotated image of HKU4r-HZAU-2020 clone: SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_Map.png HKU4r-HZAU-2020 complete sequence in fasta format: HKU4r-HZAU_2020_SRR10915173_k141_13283_del_149.fa HKU4r-HZAU-2020 annotated full clone in GenBank format: SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp.gbk HKU4r-HZAU-2020 genome only without synthetic vectors in fasta format: HKU4r-HZAU-2020_complete_genome_only.fa HKU4r-HZAU-2020 annotated genome only in GenBank format: SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_genome_only.gbk Contigs with high identity to the MERS-CoV genome (NC_019843.3) assembled from pooled SRAs SRR10915167, SRR10915168, SRR10915173, SRR10915174 in fasta format: MEGAHIT_MERS_NC_19843.3_spike_contigs.fa. Three-dimensional model of the RBD of the HKU4r-HZAU-2020 clone: HKU4r-HZAU-2020_RBD.pdb Reads in SRR10915167-8 and SRR10915173-4 mapping to the HKU4r-HZAU-2020 clone using minimap2: SRR10915167-68_73-74_k141_13283_rc_del_149_minimap2_samclip_25.bam CoronaSPAdes default de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2: SRR10915173_coronaspades_default_k141_13283_rc_del_149_minimap2.bam SPAdes careful de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2: SRR10915173_spades_careful_k141_13283_rc_del_149_minimap2.bam metaxa2 rRNA sequences de novo assembled using MEGAHIT: metaxa2_contigs.zip Reads from pooled datasets SRR10915167-8 and SRR10915173-4 aligned to S gene section of MERS-CoV genome (NC_019843.3): SRR10915167-68_73-74_NC_019843_3_S_gene_minimap2.sam Reads mapping to MERS-CoV (NC_019843.3) S gene and crossing it’s 5’ and 3’ ends showing S gene insertion into HKU4r-HZAU-2020 backbone: NC_19843.3_spike_gene_3prime_read_stats.txt NC_19843.3_spike_gene_5prime_read_stats.txt