Contig Editor for Reference Assemblies

The Contig Editor is used for viewing and editing de novo and reference assembly contigs in Assembler and as the main editor in Align to Reference. However, the Editor's interface does change depending on which function it is being used for. This page deals with the Contig Editor as used in Assembler for reference assemblies as produced by using Bowtie. Please see Contig Editor for de novo Assemblies and Contig Editor - Align to Reference to see how this is used for the other alignments.

Map tab

Coverage plot

The Map view of a reference or child contig will show details of the depth of reads in a coverage map. The coverage map shows four statistics.

Areas of zero coverage are shown in light grey.
A single plot line (default color is black) shows a running average of the number of reads at that point.
The upper shaded areas indicates the maximum value of the (default color is dark blue)
The lower shaded area indicates the minimum value of the averaged reads at that point.(default color is light blue).

The four statistics are used to provide a better visualization of coverage when viewed over an entire assembly. As you zoom into an assembly then these three values will become increasingly similar to the extent that when viewed at residue level these three plots will be close to being a single plot. Note that areas with excessively high coverage can be indicative of a repeat.

However, areas of zero coverage are always displayed even when they are disproportionate to the level of magnification. For example a region of zero coverage over a single base will always be displayed even when you are viewing a five megabase contig in its entirety. Also note that there are no areas of zero coverage in child contigs as by definition they are bounded by either end of the reference contig and/or an area of zero coverage.

For RNAseq analysis look at the Coverage tab of a contig. This contains very detailed information needed for such analysis such as RKPM and TPM for every feature.

Variant reporting in the Map View

Variants are graphically represented in two ways. There are the VCF report and SNP Report tabs and they are also graphically represented in the Map view with two plots just above the coverage map. A SNP or INDEL is represented by a vertical line. Additionally if you mouseover the SNP or INDEL plot you will see a tooltip showing the closest SNP or INDEL. The information shows

The starting base
The sequence of the SNP or INDEL represented by the difference between the reference and the reads
The quality of that score.

SNPs

If any SNPs are detected in the reference contig these will also be shown in a horizontal band just above the coverage map.

INDELs

Bowtie2 is a gapped aligner and will insert a gap into the reference or the reads where doing so results in a higher alignment score. There are two types of reported INDEL.

Blue - When the reported INDEL is present in all reads. A gap has been inserted into all reads or has been inserted into the reference. This means that there is only a single allele in the reads.
Grey - When the reported INDEL is only present in some reads. The gap may have been inserted into the reference or just a few reads. This means that there is more than a single allele in the reads.

When there is only a single allele (blue) the alignment shown in the editor tab will be adjusted. However, for multiple alleles in the reads the alignment is NOT adjusted and so may not be entirely correct at that point.

Note that if you have only a single dataset, with only one sample, in the reads then a blue INDEL would indicate it is a homozygous and a grey INDEL indicates it is heterozygous.

This is determined using the FQ column (consensus quality) in the VCF file (see VCF tab). If positive, FQ equals the phred-scaled probability of there being two or more different alleles. If negative, FQ equals the minus phred-scaled probability of all chromosomes being identical.

Misc.

Child contigs are annotated as MISC_FEATURE features in the reference contig.
For performance reasons individual reads are NOT shown in the Map View
Quality scores, displayed for child contigs, are not stored within the saved Assembly project for increased performance and to reduce file size.
You can directly run any MacVector nucleic acid analysis on the consensus sequence of the contig.
Note that the settings used to produce a Bowtie alignment are stored within the Comment Annotations field of the Reference Contig. Look at the Annotations tab of the Contig Editor to view these.