CoverageAlleles

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

The coverage band's alleles layer: the colored segment each mismatched base takes in its position's depth bar. Its filter keeps the segments whose fraction, the allele's share of the position's depth, passes; the grey depth bar shows through where a segment is left out, and everywhere under show: false. The modification bars are not allele segments: pileup.bases draws them, and nothing here hides or floors them.

Example usage#

{
  type: 'LinearAlignmentsDisplay',
  coverage: { alleles: { filter: [{ field: 'fraction', gte: 0.2 }] } },
}

{ type: 'LinearAlignmentsDisplay', coverage: { alleles: { show: false } } }

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.