Default Display

When you load genomic data, IGV displays the data in horizontal rows called tracks. Typically, each track represents one sample or experiment. For each track, IGV displays the track identifier, one or more attributes, and the data.

When loading a data file, IGV uses the file extension to determine the file format (see File Formats), the file format to determine the data type (Table 1), and the data type to determine the track default display options (Table 2).

File Format Data Type
Table 1. File Format Determines Data Type
CBS, CN, MAF, SEG, SNP, VCF Copy number
LOH LOH
GCT Gene expression or RNAi
GISTIC GISTIC data
RES Gene expression
BAM, bam.list, Goby files, PSL, SAM Sequence alignments
BED, genePred, GFF, GFF3 Genome annotations
MUT Mutation
GWAS Genome-wide association study data
IGV, WIG, HDF5 file not created with alignment processor, bedgraph Other
Cytoband, FASTA Not applicable. Cytoband and sequence files for an imported genome.

 

Data Type Default Graph Type Default Data Range Default Colors
Table 2. Data Type Determines Display Options
Copy number Heatmap -1.5 to 1.5 Blue to red
Gene expression Heatmap -1.5 to 1.5 Blue to red
Chip Bar chart None, data is autoscaled Blue
DNA methylation Heatmap 0 to 1
(methylation score)
Green
Allele-specific copy number Heatmap -1.5 to 1.5 Blue to red
LOH Heatmap -1 to 1 Blue = LOH (1)
Yellow = Retained (0)
Red = Conflict (-1)
RNAi Heatmap -3 to 3 Red to blue
GWAS Scatter plot None, data is autoscaled Chromosome colors
Other Bar chart None, data is autoscaled Blue