Additional file 6: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Boxplot of genotype concordance, non-reference sensitivity, non-reference genotype concordance and precision calculated based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers (GATK, freebayes, SAMtools) at positions where SNPs from the array were available on chromosomes 3, 6 and 28 (~50 k). The statistics of different genotype concordance metrics were measured according to Linderman et.al [20]. (PNG 239 kb)