SV Comparison in Shared Inbred Mouse Strains (Our Study vs JAX) and QC of Inversions and Duplications in Our Dataset

1. (1). The archive SV_Comparison.rar contains three subdirectories: Common, Jax_Unique, and Stanford_Unique, which correspond to structural variants (SVs) identified in the following categories, respectively: SVs shared between our study and the JAX dataset for each common inbred strain, SVs uniquely identified by JAX, and SVs uniquely identified in our study. Each of these three subdirectories further contains three folders named DEL, INS, and INV, representing deletion, insertion, and inversion events, respectively. Within each SV-type folder, there are SV comparison result files for nine representative inbred mouse strains. For example, for the strain 129S1, the corresponding files are: SV_Comparsion/Common/DEL/129S1.del.common.txt SV_Comparsion/Common/INS/129S1.ins.common.txt SV_Comparsion/Common/INV/129S1.inv.common.txt Each file lists the SVs identified in the given category and SV type.The SVs are labeled using an ID format of: 'Chromosome'-'Start Position'-'SV Type'-'SV Length'For example: chr1-3108755-DEL-66, represents a 66 bp deletion on chromosome 1 starting at position 3,108,755. (2). The nine inbred mouse strains shared between the two studies are: 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, CAST/EiJ, DBA/2J, NOD/ShiLtJ, NZO/HlLtJ, and WSB/EiJ. (3). The JAX dataset is derived from the following publication:Ferraj, A., Audano, P.A., Balachandran, P., Czechanski, A., Flores, J.I., Radecki, A.A., Mosur, V., Gordon, D.S., Walawalkar, I.A., Eichler, E.E., et al. (2023). Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. Cell Genomics, 3, 100291. https://doi.org/10.1016/j.xgen.2023.100291. 2. (1). The archive IGV_Inspection.rar contains two subdirectories: INV and SNP. The INV folder includes all inversion (INV) calls detected by three methods: Cue, Sniffles2 and PBSV. It is further divided into two subfolders: s39_small_inv and s39_large_inv, representing small and large inversions identified across all 39 inbred strains, respectively. Each of these folders contains two subdirectories: Cue and PBSV_Sniffles2, which correspond to inversion calls supported by either Cue or by PBSV or Sniffles2. Within each method-specific folder, there are two additional subdirectories: PASS and FAIL, which contain IGV screenshots (.png format) that either passed or failed manual IGV visual inspection, respectively. For small inversions, the number of reported calls is calculated as the sum of IGV-validated events in the PASS folders from Cue and PBSV_Sniffles2, i.e., 460 + 386 = 846. The number of rejected calls (failed IGV inspection) is 142 + 17 = 159. Similarly, for large inversions, the total number of reported events is 98 + 1171 = 1269, and the number of rejected events is 219 + 1039 = 1258. (2). The SNP folder contains IGV inspection results for a randomly selected set of 200 SNPs, of which 196 passed manual IGV validation. 3. The archive VaPoR.rar contains two folders: DUP and Large_INS. Within the DUP folder, there are two subfolders: Small_DUP and Large_DUP. For example, the directory VaPoR/DUP/Small_DUP/ includes three files: small_dup_s39_validated.txt (representing duplications validated by VaPoR), small_dup_s39_not_validated.txt (duplications not supported by VaPoR), and small_dup_s39_not_assessable.txt (regions too complex for VaPoR to evaluate). The number of entries in each category is 9,943 validated, 1,779 not validated and 34,039 not assessable, respectively.A similar trend is observed for large duplications, where the majority of events fall into the "not assessable" category due to genomic complexity. These results indicate that, for duplications, the proportion of regions that cannot be assessed by VaPoR is the largest. 4. The names of the 39 inbred mouse strains used in our study can be found in the README file of https://zenodo.org/records/15284878, or in the description section of https://zenodo.org/records/15110757.