Fig. 1

Mutations identified as “high impact” by SnpEff but which likely have no impact. a. An A > T mutation at position 86408706 of chromosome 1 (black arrow) was identified as a premature stop codon by SnpEff. If this mutation had happened in isolation, it would in fact result in p.Lys374* in the CLCA4 protein (bottom frame), as predicted by SnpEff. However, because there was also an A > G mutation in the adjacent nucleotide (blue arrow), the actual change would be p.Lys374Trp, a missense, not a LOF mutation. b. A “TA” insertion at position 30707229 of chromosome 17 (black arrow) was identified as a “high impact” splice_donor_variant by SnpEff. In fact, this insertion would leave a “GT” donor intact. It would simply replace one “T” for another. It is also possible that HaplotypeCaller had difficulty with the alignments in this region due to “TATA” repeats. For both 1A and 1B, mutations are reported for animal 17573 using the MacaM genome. Figures are screenshots of alignments viewed with IGV.