This track shows various rearrangements in the HPRC assemblies with respect to hg38. The types include indels, duplications, inversions, and other more complicated rearrangements. There are five tracks in the Rearrangement composite track:
All items are labeled by the number of HPRC assemblies that have the rearrangement. The indel tracks have one or two additional fields that specify how large the indel is in base pairs. For the Insertions and Deletions track there's only one number with "bp" after it. For insertions, it is the size of the insertion in hg38. For deletions, it is the size of the sequence deleted in hg38. For the Other Rearrangements track, there are two numbers given: the number of unaligned bases in hg38 and the number of unaligned bases in the HPRC assemblies.
All these tracks are built from the HPRC chains and nets. The actual instructions used to create these tracks are in the files hprcRearrange.txt and hprcInDel.txt. The first step for all the tracks is to find the orthologous sequences in each HPRC assembly for each chromosome in hg38. These sequences are called the query sequences. For each query sequence, we select the longest chain to the hg38 sequence. This is called the orthologous chain. Following are the specific methods for each track.
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