Exercise 1

Q1. You should recognise BAM files, the .fa extension for a FASTA file, and .vcf extension for a Variant Call Format file.

Q2. 197,394bp

Q3. 24858 reads, and 100%.

Q4. 16 variants: 5 deletions, 1 insertion, 1 MNP, and 9 SNPs

Q5. 20236 to 21636bp.

Q6. 13

Exercise 2

Q7. This will colour the forward read in a pair in green and the reverse read in blue.

Q8. 27 reads support the variant, no reads which don’t support the variant. You can count them, or get this from the “Coverage” figure in tablet.

Q9. There is a red box around the base next to the insertion and the base which has been inserted. This will add 1bp to the length of the strain and increase the co-ordinates for all positions after this by 1 base relative to the reference genome.

Exercise 3

Q10. 141253-157403bp

Q11. 103506-138689bp