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/15110757.1. (1). 压缩包SV_Comparison.rar包含三个子目录：Common、Jax_Unique和Stanford_Unique，分别对应以下三类鉴定得到的结构变异（structural variants, SVs）： 本研究与JAX数据集在各常见近交系小鼠中共享的结构变异、JAX独有的结构变异，以及本研究独有的结构变异。 每个子目录下均设有DEL、INS、INV三个文件夹，分别代表缺失（deletion）、插入（insertion）与倒位（inversion）事件。 每个SV类型文件夹下均包含9种代表性近交系小鼠的SV比对结果文件。例如针对品系129S1，对应的文件为： SV_Comparsion/Common/DEL/129S1.del.common.txt SV_Comparsion/Common/INS/129S1.ins.common.txt SV_Comparsion/Common/INV/129S1.inv.common.txt 每个文件均列出对应类别与SV类型的结构变异，其ID格式为：「染色体」-「起始位置」-「SV类型」-「SV长度」。例如：chr1-3108755-DEL-66，代表1号染色体上起始位置为3,108,755的66 bp缺失事件。 (2). 两项研究共有的9种近交系小鼠为：129S1/SvImJ、A/J、BALB/cJ、C3H/HeJ、CAST/EiJ、DBA/2J、NOD/ShiLtJ、NZO/HlLtJ及WSB/EiJ。 (3). JAX数据集源自以下发表文献：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., 等. (2023). 多样小鼠基因组的结构变异解析揭示转座元件介导的染色质重塑. Cell Genomics, 3, 100291. https://doi.org/10.1016/j.xgen.2023.100291. 2. (1). 压缩包IGV_Inspection.rar包含两个子目录：INV与SNP。INV文件夹包含由Cue、Sniffles2及PBSV三种方法检测到的全部倒位（inversion, INV）调用结果，进一步分为s39_small_inv和s39_large_inv两个子文件夹，分别代表在全部39种近交系小鼠中鉴定得到的小型倒位与大型倒位。 每个子文件夹下设Cue与PBSV_Sniffles2两个子目录，分别对应仅由Cue支持、或由PBSV/Sniffles2共同支持的倒位调用结果。每个方法专属文件夹下还包含PASS与FAIL两个子目录，分别存放通过IGV可视化人工质检合格与不合格的IGV截图（格式为.png）。 对于小型倒位，已报告的调用数量为Cue与PBSV_Sniffles2的PASS文件夹中经IGV验证的事件数之和，即460+386=846；经IGV质检驳回的调用数量为142+17=159。 同理，大型倒位的已报告总事件数为98+1171=1269，驳回事件数为219+1039=1258。 (2). SNP文件夹包含随机选取的200个单核苷酸多态性（single nucleotide polymorphism, SNP）的IGV质检结果，其中196个通过了IGV人工验证。 3. 压缩包VaPoR.rar包含两个文件夹：DUP与Large_INS。DUP文件夹下设Small_DUP与Large_DUP两个子文件夹。 以VaPoR/DUP/Small_DUP/目录为例，其中包含三个文件：small_dup_s39_validated.txt（代表经VaPoR验证的重复序列）、small_dup_s39_not_validated.txt（未被VaPoR支持的重复序列）以及small_dup_s39_not_assessable.txt（因区域过于复杂无法被VaPoR评估的区域）。 各类别的条目数分别为：已验证9,943条、未验证1,779条、无法评估34,039条。大型重复序列呈现类似趋势，由于基因组复杂性较高，绝大多数事件归入「无法评估」类别。上述结果表明，对于重复序列而言，无法被VaPoR评估的区域占比最高。 4. 本研究使用的39种近交系小鼠品系名称可在https://zenodo.org/records/15284878的README文件中查询，或在https://zenodo.org/records/15110757的描述部分获取。