Class 6 quiz Bold or underline correct answer

Started: Aug 17 at 9:06am

Quiz Instructions

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Flag question: Question 1

Question 1 1 pts

If a SNP call is “supported” by 20 reads, what is the depth of coverage at that SNP?

Group of answer choices

20

40

10

Depends on context

Flag question: Question 2

Question 2 1 pts

If a given region is 100,000 bases, and 10,000 reads of length 100 bp each map to to this region, what is the average fold coverage for this region?

Group of answer choices

100

20

10

Depends on context

Flag question: Question 3

Question 3 1 pts

In theory, randomly sampled reads should yield depth-of-coverage frequency histograms with what type of distribution?

Group of answer choices

Bell shaped curve

Poisson

Gamma

Gaussian

Flag question: Question 4

Question 4 1 pts

In practice, how do depth-of-coverage frequency histograms differ from purely theoretical random sampling distributions?

Group of answer choices

High ends are extended (i.e. more high coverage repeats than expected)

Generally about the same, except for minor statistical sampling variations

Low end tails are extended (i.e. more low than expected)

Both tail ends are extended (i.e. more low and more high coverage than expected)

Flag question: Question 5

Question 5 1 pts

Why might depth-of-coverage histograms deviate from expected theoretical distributions?

Group of answer choices

SNPs and other polymorphims

Repeated sequences and extremes of GC content (i.e. unusually high and low %GC)

High coverage is repeats, missing coverage is unknown

None of the above

Flag question: Question 6

Question 6 1 pts

What factors may lead to missing SNPs at low coverage?

Group of answer choices

Cannot discriminate SNP bases from read errors

Insufficient sampling of the “other”, non-reference-sequence allele

May miss SNP location due to low sampling

All of the above

Flag question: Question 7

Question 7 1 pts

In general, what best describes the relationship between depth of coverage and cost (i.e. reagents, time, etc)? Model as cost = f(coverage) with cost on the Y axis and coverage on the X axis.

Group of answer choices

Decreasing curve, initially expensive then cheaper and cheaper.

Rising curve with diminishing returns, eventually flattening out.

Linearly increasing curve with costs rising as coverage increases.

Depends on the system and cannot be generalized

Flag question: Question 8

Question 8 1 pts

In general, what best describes the relationship between depth of coverage and derived information (e.g. SNPs and other polymorphisms called)? Model as info = f(coverage) with info on the Y axis and coverage on the X axis.

Group of answer choices

Logarithmic curve, with decreasing yield for added coverage

Linearly increasing curve, with more information added with additional coverage

Decreasing curve, with additional coverage only improving accuracy

Depends on the system and cannot be generalized

Flag question: Question 9

Question 9 1 pts

If a base in a read has an associated Phred score of 30, what are the odds that it is incorrect ?

Group of answer choices

1%

0.1%

1 in 10000

Less than 1 in 10000

Flag question: Question 10

Question 10 3 pts

In light of the relationships between cost and effort and derived information, how might you choose an appropriate level of coverage for a particular new study? Assume both the biological system being explored and specific technologies are unfamiliar to you.

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Flag question: Question 11 short essay

Question 11 4 pts

Define the following terms using the rediscovery of known SNPs using a novel technology as an example: True Positive = ? False Positive = ? True Negative = ? False Negative = ?