The whole point behind Next Generation Sequencing is to get a lot of redundant and cheap raw data, but with some errors. This way you sequence the same base of

The whole point behind Next Generation Sequencing is to get a lot of redundant and cheap raw data, but with some errors. This way you sequence the same base of the genome say 10 times or more. If 9 of them are the same as the reference, and 1 is another base (and this base is low quality), the Variant Caller can be confident that was a sequencing error, and the position is the same base as the reference. But if you have 5 reference and 5 of other base, it's probably heterozigous for that position. If you have more of other base, is homozigous for that other base.