What is a sequencing read?
A short DNA fragment produced by a sequencing machine.
What is reference mapping?
Aligning sequencing reads to a known reference genome.
Why is quality control important?
To remove low-quality reads that can cause false SNPs.
What does a gap in read coverage indicate?
An indel (insertion or deletion).
Can you tell indel direction from mapping alone?
No, you cannot determine insertion vs deletion without additional information.
What is a SNP?
A single nucleotide difference between genomes.
Where can SNPs occur?
In coding regions or intergenic regions.
What is a synonymous SNP?
A SNP that does not change the amino acid.
Impact of synonymous SNPs?
Usually neutral with minimal effect.
What is a missense SNP?
A SNP that changes one amino acid.
Impact of missense SNPs?
Variable; can be neutral or harmful.
What is a nonsense SNP?
A SNP that creates a premature stop codon.
Impact of nonsense SNPs?
Truncated protein and usually loss of function.
Which SNP type has the greatest impact?
Nonsense SNPs.
Why are nonsense SNPs rare?
They are often deleterious and removed by selection.
What are indels?
Insertions or deletions of nucleotides.
How do indels affect genes?
They can disrupt or delete genes.
What file format stores mapped reads?
SAM or BAM.
What file format stores variants?
VCF.
What does TRAMS do?
Annotates SNPs as synonymous, missense, or nonsense.
What is de novo assembly?
Building a genome without a reference.
Why is de novo assembly difficult?
Repeats and short reads cause fragmentation.
How do paired-end reads help?
They help span repeats and improve mapping.
Exam rule for mapping images?
Gap = indel; mismatch = SNP.
