1. If we assume there are no sequencing errors, are you more inclined to speculate that Locus 1 is a germline or somatic variant? Why?
   • Locus 1 is more likely to be a somatic variant because a germline variant would either manifest as a roughly 50:50 ratio of reference (“A”) to alternate (“T”) alleles, or all alternate alleles. However, it can be difficult to draw conclusions from such low sequencing depth.
2. Given the existence of sequencing errors, how confident are you that Locus 1 represents a heterozygous locus in the germline?
   • Not very confident: In general for most heterozygous germline mutations we would expect roughly equal reference and alternate alleles, or all alternate alleles, from our sequencing, and the ratio we see much more lopsided; however with so few reads a sequencing error isn’t out of the question
3. Given the existence of sequencing errors, how confident are you that Locus 1 represents a polymorphic locus in a somatic tissue?
   • Still not very confident as we only have 2 reads of support, however it is more in-line with expectations for a somatic polymorphism rather than a germline variant, because somatic polymorphism don’t need to have a 50:50 or 100:0, they can be any fraction
4. How confident are you that Locus 2 is homozygous?
   • While the evidence is suggestive, we are not particularly confident with such a low sequencing depth
5. What additional information might you want in order to better assess these loci?
   • More sequencing depth would allow us to better assess these loci and have more confidence in any conclusions we might draw