Lecture 14-MT2

Question 1

What is the core genome?

Answer 1

Genes found in all members of a bacterial species
Common DNA
-critical genes
-genotyping
-phylogenetics

Question 2

What is the accessory genome?

Answer 2

Genes found in some but not all members of species

Question 3

Pan genome

Answer 3

All genes found in all members of species
-Core + accessory
-plasmids
-mobile elements
-phage

Question 4

What is De novo genome assembly

Answer 4

From new/ from scratch
-reconstruct the original genome from the sequence reads only

Question 5

What is a read?

Answer 5

millions of short sequences

Question 6

What is a contig?

Answer 6

Few long sequences that go in a certain order but we do not know the order it comes in the genome

Question 7

What is coverage?

Answer 7

number of reads

Question 8

How to find the average coverage?

Answer 8

Total bases/ consensus length

Question 9

How to find total bases?

Answer 9

Number of reads x Base pair length

Question 10

To confidently assign a base pair what percent does it need to be?

Answer 10

75%

Question 11

What types of genomes is Breseq used for?

Answer 11

-haploid genomes
-<1000 mutations expected

Question 12

True or false: for $ breseq all reads come from any individual

Answer 12

False
$ breseq have reads from a single clone
$ breseq -p have reads from any individual

Question 13

Breseq mutation: RA

Answer 13

Substitutions, short indels

Question 14

Breseq mutation: JC

Answer 14

Bigger indels

Question 15

Breseq mutation: MC

Answer 15

large deletions or low coverage regions