Examples of validated mutations discovered in mutant exome data . The bloodline mutation is a recessive mutation that causes a distinctive dorsal epidermal defect and tooth pulp necrosis. Exome sequencing revealed a G to A mutation in Map3K11 (mitogen-activated protein kinase kinase kinase 11). (a) PCR and sequencing of additional mutant (bloodline/bloodline) and unaffected (+/+ or +/-) animals provided additional support for this putative mutation. The 'Cleft' mutation is an ENU mutation that arose on C57BL/6J. The mutation causes a dominant craniofacial phenotype and recessive perinatal lethality with characteristic cleft palate. (b) Sanger sequencing confirmed the presence of two closely linked mutations in multiple cleft/+ and cleft/cleft samples and the absence of these mutations in +/+ littermate samples. (c) Of the two mutations found, the intron mutation has the potential to cause splicing defects, although it is less likely to contribute to the phenotype since RT-PCR shows no indication of defective splicing mutant samples. The 'Sofa' mutation is a spontaneous mutation that arose on C57BL/6J, causing a dominant craniofacial phenotype and recessive perinatal lethality. (d) Sanger sequencing of heterozygous and control samples confirmed the presence of a 15-bp deletion in Pfas, FGAR amidotransferase. (e) Reads from the mutant, deletion-bearing allele successfully mapped to Pfas using BWA (Burrows-Wheeler aligment tool) and the deletion was called using SAMtools  with an allele ratio of 0.2.