Paired End Arrow Colors in the Strategy View

The lower half of the Strategy View displays arrows representing the individual sequences in the contig.

The point of the arrowhead represents the 3’ end and the tail represents the 5’ end. Solid arrows pointing right represent sequences assigned to the top strand of the consensus sequence. Dash-lined arrows pointing left represent sequences assigned to the bottom (complementary) strand of the consensus sequence.

When paired end data are present and correctly specified, the arrows in the lower half of the Strategy View will use the following color coding:

•      Black – Represents reads for which no paired data information is available or recognized.

•      Green – Represents paired reads in the same contig whose assembly locations are consistent with the Pair Specifier parameters.

•      Dark Blue – Represents paired reads in different contigs in the scaffold whose assembly locations are consistent with Pair Specifier parameters.

•      Pale Blue – Represents paired reads in different contigs (in the same or different scaffolds) whose assembly locations could be consistent with Pair Specifier parameters if the contigs were rescaffolded or reordered. The number appearing next to the pale blue arrows indicates which contig the other member of the pair is in.

•      Orange – Represents paired reads in different contigs whose assembly locations or orientations are inconsistent with Pair Specifier parameters, even if the contigs were rescaffolded or reordered.

•      Red – Represents paired reads in the same contig whose locations or orientation are inconsistent with Pair Specifier parameters.

•      Pink – Represents split reads in the same contig whose locations or orientation are inconsistent with Pair Specifier parameters.