Is short-read sequencing a haploid or diploid sequencing?

[choyk1]

Is short-read sequencing a haploid or diploid sequencing?

If it is a diploid sequencing, does the read containing a heterozygous indel show similar pattern as Sanger sequencing (mixed peaks on tail)? For example, mixed color dots on the later cycles in illumina sequencing?

[swbarnes2]

Is short-read sequencing a haploid or diploid sequencing?

If it is a diploid sequencing, does the read containing a heterozygous indel show similar pattern as Sanger sequencing (mixed peaks on tail)? For example, mixed color dots on the later cycles in illumina sequencing?

No. The read itself is not mixed. Each cluster is based on a single piece of DNA, so if you have a heterozygote that is half A and half G, each cluster will show one or the other. But that position will be covered by many reads, and you'd expect half the reads to show the A, and half to show the G.

When aligning, if your reference has an A, expect some bias, because reads with the A and the max number of allowable errors will align, but reads with the G and the same number of errors will not.