ONALETHATA BAOPEDI

1700111117

College of Science
Department of Biology and Biotechnological Science

17001355
BIOL 306
Sequence Mapping and Variation
[50 points]
The figure below shows the gene locations for the human mitochondrion DNA(mtDNA) from a
healthy individual (The sequence is stored in the provided file mtDNA_Healthy_Individual.fna)

Figure 3.1 Gene Locations on Mitochondrion from healthy

individual

You have been provided with the reads file HumanmtDNA_Reads.fastq that you should align to
the reference genome in the file mtDNA_Healthy_Individual.fna just like you did in class.
1. Using the Slides from class, find any variants that may exist between the reference genome
and the sequenced reads. Please provide a labeled table with all the variants you identified. [25
points]
2. What is a transition mutation? [1 point]
A mutation whereby a purine is changed in to another purine or a pyrimidine is changed in to
another pyrimidine

3. What is a transversion mutation? [1 point]

When a single purine is converted to a pyrimidine or vice versa

4. How many transversion mutations can you identify on your table from Question 1. [2 points]
There are 5 transerse mutations identified
5. How many transition mutations can you identify on your table from Question 1. [2 points]
11 transition mutations were identified

6. Using Figure 3.1 and your table of variants, how many genes have mutations? [2 points]
10 genes have mutations
7. Using Figure 3.1 and your table of variants, how many protein coding genes have variants? [2
points
8 protein coding genes have variants

Mutations in mitochondrion genes can lead to liver diseases, hearing impairments, visual
impairments, and cognitive impairments. For this Lab, we will focus on known mutations that
cause hearing and visual impairment in individuals. The table below gives such mutations.

Table 3.1 List of mtDNA Point mutations known to cause

hearing and visual impairment in humans

8. The point mutations shown in Table 3.1 correspond to what genes from Figure 3.1? [5 points]
Table 1 showing point mutations that corresponds with different genes

9. Do the variants from your table have any of the mutations shown in Table 3.1 and what are
these mutations and type of impairments (if any)? [5 points]
Table 2 showing mutations and their types of mutations
VARIANT LOCATION TYPE OF MUTATION TYPE OF IMPAIRMENT
1555 A-G: transition mutation hearing
7445 A-C: transversion mutation Hearing
7445 A-G: transition mutation Hearing
7445 A-G: transversion mutation hearing
8993 T-G :Transversion mutation visual
10. Individuals with the mutation A to G at locus 1555 on their mtDNA experience irreversible
hearing loss when given the following antibiotics: gentamycin, tobramycin, amikacin,
kanamycin, and streptomycin. If a Father has this mutation, would you give his child one of the
antibiotics that we just mentioned? Please explain why. [3 points]
These antibiotics can be recommended to a child without any threat since this mutated mRNA
can only be maternally inherited thus a mutation from a father can not affect a child.

11. Based on your table of variants from Question 1. Which of the two datasets
(HumanmtDNA_Reads.fastq and mtDNA_Healthy_Individual.fna) has a point mutation that
leads to hearing impairment? [2 points]
Among this two datasets , humanmtDNA_Reads.fastaq contains a lot of point mutations that
leads to hearing impairment , these mutations are found at position 7444 and 12236