qbb2024-answers

QB Lab Week 1 Exercise

Q1.1

1Mbp genome x 3 = 3 Mbp = 3,000,000 bp 3,000,000 bp / 100 bp = 30,000 reads

30,000 100bp reads are needed to sequence a 1Mbp genome to 3x coverage.

Q1.4

1. 49535 base pairs had 0 coverage.
2. This largely matches the poisson expectations but could be better. The normal distribution fits the data but also could be better.

Q1.5

1. 80 base pairs had 0 coverage.
2. This matches the poisson expectations well, better than the 3x coverage plot. The same can be said for the normal distribution.

Q1.6

1. 12 base pairs had 0 coverage.
2. This matches the poisson expectations very well. The poisson distribution and the normal distribution match the best of all 3 coverages we simulated.

Q2.4

dot -Tpng edges.dot > ex2_digraph.png

Q2.5

A T T C A T T C T T A T T G A T T T

Q2.6 To accurately reconstruct the sequence of the genome it would take sequencing of longer reads.