Introduction to the Data Set
Figure 1
Created in BioRender.com
Figure 2
Input File Format
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
{alt=‘Figure showing the qtl2 control file’, width=75%}
Calculating Genotype Probabilities
Figure 1
{‘a chromosome with two typed markers labeled BR and RR with a locus of unknown genotype between them’}
Figure 2
Figure 3
{‘a web page showing R data structures including one-dimensional vectors and lists, two dimensional dataframes and matrices, and n-dimensional arrays’}.
Figure 4
Figure 5
Figure 6
{‘a table showing the probabilities for each of 36 genotypes in the Diversity Outbred followed by a second table showing probabilities for each of the 8 founder alleles’}
Performing a genome scan
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Calculating A Kinship Matrix
Figure 1
Performing a genome scan with a linear mixed model
Figure 1
Figure 2
Figure 3
Performing a genome scan with binary traits
Figure 1
Figure 2
Figure 3
Performing a permutation test
Figure 1
Figure 2
{alt=“Comparison of significane threholds”,width=“50%”}
Figure 3
{alt=“Figure showing decreasing variance of significance threshold estimates with increasing permutations”,width=75%}
Finding QTL peaks
Figure 1
Estimating QTL effects
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Figure 11
Integrating Gene Expression Data
Figure 1
Figure 2
Figure 3
Figure 4
QTL Mapping in Diversity Outbred Mice
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Figure 11
Figure 12
Figure 13
{alt=“Figure showing haplotypes being used to impute founder SNPs onto DO genomes.”,width=75%}
Figure 14
{alt=“Plot showing LOD of each SNP in QTL interval”,width=100%}
Figure 15
{alt=“Plot showing LOD of each SNP in QTL interval with genes below”,width=100%}
Figure 16
{alt=“Plot showing LOD of each SNP in QTL interval with genes below and strain distribution pattern above”,width=100%}
Figure 17
{Figure showing LOD plots of Sult3a1 & 2 and CAST-specific haplotype effects}
Figure 18
{Figure showing that Sult3a1 & 2 are paralogs}
Figure 19
{alt=“Ensembl viewer showing genes and structural variants under that chromosome 10 QTL peak”,width=100%}
Figure 20
{alt=“Ensembl viewer showing genes and structural variants under that chromosome 10 QTL peak”,width=100%}
Figure 21
{alt=“Figure showing CAST with a duplication at the Sult3a1/2 locus.”,width=100%}
Figure 22
{alt=“Figure showing benezene metabolism pathways”,width=100%}
Figure 23
{alt=“Figure showing mice carrying the CAST allele being protected from benezene toxicity”,width=100%}