general but important concepts

[dejavu2010]

I have questions about some concepts:
1. In the reference human genome, i assume the position is relevant to the end of chromosome, which some times refers to pter, qter. I guess all position in the genome refers to pter, the first base is 0 or 1? how to decide pter or qter when the first time to sequence human genome? The chromosome is diplot, how to get haplot? The chromosome is important since there will be position 123456 on chromosome 1...n.

[syfo]

Regarding your first question (I am not sure I understand the others) about numbering the first base, the answer depends on the format: in BED files the first nucleotide is assigned a "0" while in GFF files it is "1".
http://genome.ucsc.edu/FAQ/FAQformat.html