I've used a samtools, bcftools pipeline to generate a diploid consensus sequence. The consensus sequences are in fastq format. I expected that I'd get two sequences in the fastq files - one for each homologous chromosome. But when I open them, I can only see a single sequence identifier. How does FASTQ encode which base belongs to which homologous chromosomes? I can see a long string of n's in the middle of the sequence. Is that where they're separated?
Edited for clarity