How is an X chromosome encoded into a fasta string?

Question

A human "X" chromosome has a centromere and two "identical" chromatids. If the chromatids are not identical, this fact is not assembled, correct?

The fasta string for a chromomsome is actually representing just one of the chromatids, correct?

So from my understanding, for diploids, the fasta chromosome is actually a mix of 4 chromatids: 2chromatids * 2 pairs of chromosomes into one string. Which for some heterozygous nucleotides (same percentage of each allele) will just be randomly selected from the reads as the correct one.

(unless we are talking about some methods like 10x that can distinguish between chromosomes pairs)

I was thinking which side of the X is read first into the fasta string, and I came to the above conclusion.

Answer 1

So, the two chromatids you see only during meta-phase of replication. In more "regular" state of a cell, there are only the two haplotypes (in the case of a diploid organism)

Well, and regardless of the ploidy, we usually aim for a haploid (monoploid) representation, so it is usually exactly as you say - an arbitrary one of the two states on each heterozygous site is chosen.

However, there are also approaches to phase genomes (to sort which alleles are on which haplotypes). That is possible not just with 10x, but also with long reads (to certain extend) or using trio-binning - a strategy to sequence two parents and the offspring.

However, even phased genomes still contain the reference (fasta) in a haploid state and usually provide the alternative haplotype as a second fasta file.

For the record, these apply to all chromosomes, not just the X.