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Tip: You can also index BAM and FASTA files the same way inside of IGV if you haven't already created indexes for them. But, it's usually easier and quicker to do this on the command line.
Exercises
Check out the rbsA gene region? What's going on here?
Expand Answer Answer There was a large deletion. Can you figure out the exact coordinates of the endpoints?
Navigate to coordinate 475,288. Compare the results for different alignment programs and settings. Can you explain what's going on here?
Expand Answer Answer There is a 16 base deletion in the gltA gene reading frame.
What is going on in the pykF gene region? You might see red read pairs. What does that mean? Can you guess what type of mutation occurred here?
Expand Answer Answer The read pairs are discordantly mapped. There was an insertion of a new copy of a mobile genetic element (an IS150 element) that exists at other locations in the reference sequence.
Workflow 2: Viewing Human Genome Data in IGV
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