PileupMismatches

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the alignments plugin. View source.

The pileup's mismatches layer: how each read differs from the reference, as per-base mismatches, insertion markers and deletion bars, and the opacity each mismatched base takes from its quality. The line joining a spliced read across its introns draws either way, since it shows the exon blocks are one read (PILEUP_MARKS).

Example usage#

{ type: 'LinearAlignmentsDisplay', pileup: { mismatches: { show: false } } }

{
  type: 'LinearAlignmentsDisplay',
  pileup: { mismatches: { encoding: { opacity: 'baseQuality' } } },
}

Config slots#

A setting written to it names members one by one: a member left out stays as it is, and null resets one. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.