A1.2

Question 1 Single best answer Level 1 1 point

A FASTQ record is organized into four lines. Which line contains the per-base quality scores?

  1. The third line
  2. The fourth line
  3. The first line
  4. The second line

Question 2 Single best answer Level 1 1 point

In a FASTA file, what does a line that begins with the > character contain?

  1. A descriptive identifier for the sequence that follows
  2. A separator marking the end of one record
  3. A per-base quality score for each nucleotide
  4. The nucleotide or protein sequence itself

Question 3 Single best answer Level 2 1 point

The same set of reads can be stored as either FASTA or FASTQ. What information does the FASTQ file contain that the FASTA file does not?

  1. The amino acid sequence of the encoded protein
  2. The nucleotide sequence of each read
  3. A header line identifying each record
  4. A per-base quality score for every nucleotide

Question 4 Single best answer Level 2 1 point

Illumina adds one nucleotide per cycle, each carrying a fluorescent reversible terminator. What does that terminator do during a cycle?

  1. It permanently stops synthesis so each strand reports only one base
  2. It tags each cluster so overlapping signals can be told apart
  3. It blocks extension for imaging, then is cleaved for the next base
  4. It attaches the DNA fragment to the flow cell surface

Question 5 Single best answer Level 3 1 point

A base call’s Phred quality score rises from Q20 to Q30. Using \(P = 10^{-Q/10}\), how does its probability of being wrong change?

  1. Its error probability rises to about ten times the previous value
  2. Its error probability falls to about one tenth of the previous value
  3. Its error probability falls to about one hundredth of the previous value
  4. Its error probability falls to about one half of the previous value

Question 6 Single best answer Level 3 1 point

A DNA library has inserts of about 50 bp and is sequenced with 100 bp reads. Will adapter sequence appear in the reads?

  1. No; adapters are stripped off before the run, so they never appear in a read
  2. No; the read is shorter than the insert, so it stops before the adapter
  3. Yes; the read is longer than the insert, so it reads through into the adapter
  4. Yes; adapter sequence is present in every read no matter the sizes

Question 7 Single best answer Level 4 1 point

A FastQC report for a single-organism library shows three things at once. Per Base Sequence Quality stays in the green zone across the whole read. Per Base Sequence Content lines are flat and parallel. Per Sequence GC Content shows two clear peaks instead of one. What is the most likely explanation?

  1. The library is clean and needs no further checking
  2. Priming bias in the first few bases of the reads
  3. Signal decay at the 3-prime end of the reads
  4. Contamination or a mix of sequences from more than one source

Question 8 Single best answer Level 4 1 point

A FastQC report shows Per Base Sequence Quality in the green zone for roughly the first 60 bp, then sliding into the yellow and red zones toward the end of the read. Per Sequence GC Content is a single clean peak. Which problem is indicated, and which preprocessing step addresses it?

  1. Declining base quality at the 3-prime end; trim low-quality bases from the 3-prime end
  2. Priming bias at the 5-prime end; trim bases from the start of each read
  3. Insufficient sequencing depth; resequence the library at higher coverage
  4. Contamination from a second organism; discard the entire run
Back to top