finswimmer is correct about MT, but not quite right about the CHR_HSCHR17_2_CTG5 style names. These names refer to patches and haplotypes.

Haplotypes are regions of significant difference between individuals. The best way to represent them is as different bits of genomic sequence, rather than as variants, because they are so very different. Once example of these is the MHC locus. These were part of the genome (GRCh38) when it was first released and are official parts of the reference assembly.

Patches are genomic regions that were added to the genome after it was released. They can be fix patches, which are repairs in the genome, replacing dodgy sequencing or assembly on the main assembly. Or they can be novel patches, essentially new haplotypes that have since been discovered. Patches are added in patch versions on the genome (eg GRCh38.p11), but they were all still created and added by the Genome Reference Consortium and are official parts of the reference genome assembly.

Hello xiaohuichen03,

MT is the mitochondrial genome. The other are so called alternate assembly. These references doesn't make it into the official reference of the classical chromosomes as they haven't enough evidence, but where found in some individuals.

fin swimmer

A little discuss I started here on what to do with those according to your analysis (in mouse)

See also