SBX alignment options

This page describes additional options for viewing SBX read alignments.

Enabling SBX options#

SBX alignment options are enabled from the Alignments tab of the user preferences window. These options are applied to alignment tracks with experiment type "SBX".

Insertion recoloring#

The "INDEL Coloring uses grey" option enables insertions to be colored based on the base qualities of the inserted bases and the bases adjacent to them. By default, the color of insertions will be purple. However, there are two alternate colors which will be used if some or all of the relevant bases are discordant, meaning that the two sequencing reads of the hairpin duplex molecule disagreed on that base:

1. Light grey (#b4b4b4) is used if all inserted bases are discordant (denoted by having base quality less than or equal to 10)
2. Dark grey (#8c8c8c) is used if at least one inserted base is discordant, or if either of the following is true:
   • A base immediately adjacent to the insertion is discordant
   • There is a homopolymer substring of the read which fully contains the insertion and which has at least one discordant base
     A few examples of this recoloring can be seen in the image below:
     
     

Coloring or hiding SBX simplex tails#

Some SBX reads will have a simplex tail, where one read of the hairpin molecule extends past the other. This results in the entire end of the read being based on a single sequencing pass rather than the consensus of two passes. The bases in these tails have base qualities between those of concordant bases and discordant bases, and can be either highlighted or hidden with the SBX-specific IGV options of "Simplex tail coloring" and "Hide simplex tails". When these options are enabled, IGV detects tails on either end of reads which have base qualities in the range (10, 30], and can either highlight them in pink or hide them entirely.

Example of highlighting simplex tails:

Example of hiding simplex tails:

References#

Sequencing by expansion (SBX) technology