Supporting sequencing data for the recovery of the complete Hubei virga-like virus 2 genome

Note: All coordinates are reported relative to the MW435005.1 (USA, 2017) genome. 1.File name: file_sort_paired_40.bam Description: This BAM file contains the reference-guided assembly of the complete genome recovered from Oaxaca sample 40, using the USA Hubei virga-like virus 2 genome as the reference sequence. The recovered insertion, which is absent from the reference genome, can be observed between genomic coordinates 4911-5128. 2. File name: file_sort_paired_33.bam Description: This BAM file contains the reference-guided assembly of the complete genome recovered from Oaxaca sample 33, using the USA Hubei virga-like virus 2 genome as the reference sequence. The recovered insertion, which is absent from the reference genome, can be observed between genomic coordinates 4911-5128. 3.File name: Region_40_4911_5128.bam Description: This BAM file corresponds to the trimmed genomic region containing the insertion (coordinates 4911-5128) recovered from Oaxaca sample 40. It was generated to facilitate detailed visualization of the read depth across the insertion. Additional nucleotides are visible at both ends of the recovered region because sequencing reads extend beyond the insertion boundaries, resulting in partial alignment inside and outside the insertion. 4.File name: Region_33_4911_5128.bam Description: This BAM file corresponds to the trimmed genomic region containing the insertion (coordinates 4911-5128) recovered from Oaxaca sample 33. It was generated to facilitate detailed visualization of the read depth across the insertion. Additional nucleotides are visible at both ends of the recovered region because sequencing reads extend beyond the insertion boundaries, resulting in partial alignment inside and outside the insertion. 5.File name: alignment_allsequences.aln Description: This file contains the whole-genome multiple sequence alignment including the recovered genomes, genomes downloaded from NCBI, and the reference genome. The alignment highlights the genomic region between coordinates 4911 and 5128, where an insertion is present in all recovered and NCBI genomes but absent from the reference genome. 6.File name: trimmed_alignment_without_insert.treefile Description: This file contains the phylogenetic tree generated with IQ-TREE2 using the whole-genome alignment after removing the insertion region. 7.File name: alignment_with_insert.treefile Description: This file contains the phylogenetic tree generated with IQ-TREE2 using the complete whole-genome alignment, including the insertion region. 8.File name: paired_results_33.bam Description: BAM file containing the recruited reads from BioProject PRJNA318834 using the Hubei virga-like virus 2 genome assembly recovered from Oaxaca sample 33 as the reference genome. 9.File name:paired_results_40.bam Description: BAM file containing the recruited reads from BioProject PRJNA318834 using the Hubei virga-like virus 2 genome assembly recovered from Oaxaca sample 40 as the reference genome. 10.File name:paired_results_usa.bam Description: BAM file containing the recruited reads from BioProject PRJNA318834 using the Hubei virga-like virus 2 genome GenBank accession MW435005.1 as the reference genome.