PReS-FINAL-2286: Mastitis in an adolescent patient with juvenile systemic lupus erythematous

Additional file 6: Figure S3. Accuracy of BayesB models with varying π values

Information for the 50k MD and 600k HD panels in the analyses.

<p>Information for the 50k MD and 600k HD panels in the analyses.</p

Average computing time in hours for BayesB, anteBayesB or BayesN with 1.0 or 0.2 Mb windows for two values of <i>π</i> or <i>π</i>_<i>i</i> corresponding to 300 QTL each being associated with either 2 (red) or 10 (blue) SNP markers.

<p>The capped error bar indicates the standard deviation from 8 replicates of common and 8 replicates of rare QTL scenarios.</p

Average linkage disequilibrium (LD) between any two SNPs within 0.2 Mb distance across the genome.

<p>The shaded areas indicate one standard deviation departures from the average. The average distance between adjacent SNPs for the MD 50k and HD 600k SNP panel are indicated as broken vertical lines.</p

Regression coefficient of true on estimated breeding values using BayesB, anteBayesB or BayesN with 1.0 or 0.2 Mb windows for two values of <i>π</i> or <i>π</i>_<i>i</i> corresponding to 300 QTL each being associated with either 2 (red) or 10 (blue) SNP markers.

<p>Results are separated for common (row 1) versus rare (row 2) QTL alleles with the MD 50k (column 1) versus HD 600k (column 2) SNP panel. Dots represent regression coefficients from each of the eight replicates, and the bar indicates the mean. Regression coefficients closer to one (dashed horizontal line) reflect less prediction bias.</p

The accuracy of prediction using BayesB, anteBayesB or BayesN with 1 or 0.2 Mb windows for two values of <i>π</i> or <i>π</i>_<i>i</i> corresponding to 300 QTL each being associated with either 2 (red) or 10 (blue) SNP markers.

<p>Results are separated for common (row 1) versus rare (row 2) QTL alleles with the MD 50k (column 1) versus HD 600k (column 2) SNP panel. Dots represent accuracies from each of the eight replicates, and the bar indicates the mean.</p

The posterior mean of number of the SNPs (light bar) and windows (dark bar) with nonzero effects from BayesB, anteBayesB or BayesN with 1.0 or 0.2 Mb windows.

<p>Results are separated for <i>k</i> = 2 (row 1) versus <i>k</i> = 10 (row 2) SNPs associated with each of the 300 QTL with the MD 50k (column 1) versus HD 600k (column 2) SNP panel. The capped error bar indicates the standard deviation of the posterior means from 8 replicates of the scenario with common and 8 replicates of the scenario with rare QTL alleles. The red dashed line shows the number of QTL simulated, which was 300.</p

MOESM7 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

Additional file 7: Figure S4. Accuracy of BayesN models with varying Π values

Additional file 1 of Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Additional file 1: Fig. S1. SNP effects cross the whole genome at the heritability of 0.1. Fig. S2. SNP effects cross the whole genome at the heritability of 0.3. Fig. S3. SNPeffects cross the whole genome at the heritability of 0.5

MOESM5 of Population structure and genomic inbreeding in nine Swiss dairy cattle populations

Additional file 5: Figure S4. Distruct plot of the Admixture results for the nine Swiss cattle populations. Cross-validation error was lowest for k = 9 and 10, which indicates that k = 9 or 10 is the optimal number of clusters