Supporting Information for Simecek et al., 2015

Files in this Data Supplement:

• Supporting Information - Figure S1 and descriptions of Tables S1-S6 (PDF, 326 KB)
• Figure S1 - IGV Browser screen with the coverage of exome sequencing in the Icam2 region. (PDF, 283 KB)
• Table S1 - MDA and exome sequencing file identifiers and quality measures: number of reads, target fold coverage and percentage of target covered with >= 10 reads (exome sequencing); percentage of MDA probesets' calls (2 B6 alleles / 2 non-B6 alleles / heterozygous / drop in intensity / no call). (.xlsx, 13 KB)
• Table S2 - List of SNPs among substrains identified by exome sequencing annotated by Ensembl Variant Effect Predictor. Coding SNPs are highlighted in bold. If the SNP is covered by more than one gene or transcript, all possible consequences are listed (separated by "//"). (.xlsx, 80 KB)
• Table S3 - List of short indels identified by exome sequencing annotated by Ensembl Variant Effect Predictor. Coding indels are highlighted in bold. If the SNP is covered by more than one gene or transcript, all possible consequences are listed (separated by "//"). (.xlsx, 32 KB)
• Table S4 - List of SNPs and VINOs from Mouse Diversity Array analysis annotated by Ensembl Variant Effect Predictor. If the SNP is covered by more than one gene or transcript, all possible consequences are listed (separated by "//"). (.xlsx, 17 KB)
• Table S5 - List of (long) deletions and extra copies identified by Mouse Diversity Array copy number variation analysis. (.xlsx, 12 KB)
• Table S6 - Rare allele frequency in 5 NOD substrains. Only loci with >100 reads for each strain are included. Grey cells indicate variants that were not represented as a predominant allele in any of the 5 strains (included in the % sequencing error calculation), pink cells are variants that matched the predominant allele in one or more strains in the opposite PCR pool (included in the inter-pool error calculation), and yellow cells are variants matched the major allele of other substrains in the same PCR pool (included in the itra-pool jumps calculation). Note that some allele data fall into more than a single class. Red text indicates class (1) and (2) variants at >1 rare allele read count. (.xlsx, 14 KB)