How to statistically quantify the coverage of features in the data?

1. How do you calculate coverage depth?
2. How do you calculate sequence coverage?
3. How do you calculate average coverage in BAM?
4. How does Samtools calculate coverage?

How do you calculate coverage depth?

The coverage depth of a genome is calculated as the number of bases of all short reads that match a genome divided by the length of this genome.

How do you calculate sequence coverage?

We can use the coverage as the average number of occurrences and y as the exact number of times a base is sequenced, and then compute the probability that would happen: P(Y=3) = (6.33 × e-6.3)/3! = 0.077 Of course, this is the value for exactly 3.

How do you calculate average coverage in BAM?

If you want to get the average coverage: add up the product of bases per coverage [ 2* 4+3* 28+4* 10+... ] and divide by the total number of bases [137928].

How does Samtools calculate coverage?

This application computes the depth at each position or region andproduces a histogram or table of coverage per chromosome from an input BAM file. The input BAM files hast to be sorted by position or name, otherwise it will give an error. Otherwise the output will be a table.