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Changes the value represented by each pixel of track data.

At all but the lowest zoom levels, each pixel represents a significant amount of data. IGV divides the data to be displayed into "windows" of equal length each corresponding to a single pixel, summarizes the values across each window, and then displays the summarized values in the track. Select the function IGV will use to summarize the values.

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Displays overlapping features, such as different transcripts of a gene, on one line or multiple lines or condensed (squished).  more...

The selected feature, defined by feature start and end bounds, is used in a BLAT (BLAST-like Alignment Tool) search within the given genome as detailed on the BLAT Search page.

• Search with sequences of up to 8 kb in length.
• The default BLAT server is hosted at the UCSC Genome Browser and supports most UCSC derived genomes including human and mouse genomes. Change the default search server in Advanced Preferences.

Sorts alignments by start location, strand, base, mapping quality, sample, read group, or insert size as defined in the SAM/BAM file format and detailed below in Color alignments. 

When sorting by base, alignments which span a base with a splice, i.e. do not actually cover the base, now appear at the bottom.

Additionally, repeat the most recent sort with hotkey ctrl-s.

Colors alignments by the following options:

• No color displays reads in gray. Low mapping quality reads are still represented in unshaded white.
• Insert size details are here.
  • Blue is for inserts that are smaller than expected.
  • Red is for inserts that are larger than expected.
  • Inter-chromosomal rearrangements are color-coded by chromosome.
• Pair orientation details are here.
  • Shades of green to blue show structural events of inversions, duplications, and translocations within a chromosome.
• Insert size and pair orientation. Translocations on the same chromosome follow the color-coding schema for pair orientation, whereas translocations between two chromosomes follow the color-coding schema for insert size. If a read pair has both unexpected orientation and insert-size, the orientation color schema is used.
• Read strand in pastels, red for positive rightward (5' to 3') DNA strand, blue for negative leftward (reverse-complement) DNA strand, and grey for unpaired mate, mate not mapped, or otherwise unknown status.
• First-of-pair strand assignment is dependent on RNA transcript directionality and is useful for directional libraries. Displays reads or read pairs in which the forward read is first (F1 or F1R2) in red and reads or read pairs in which the reverse read is first (R1 or R1F2) in blue. Unknown status is in gray.
  • For a given transcript, non-directional libraries will show a mix of red and blue reads aligning to the locus.
  • Directional libraries will show reads of one color in the direction matching the transcript orientation.
• Read group is designated in the SAM format file header section under @RG. E.g., for Illumina reads, RG typically groups reads from a lane.
• Sample is a tag designated in the SAM format file header section under @RG that specifies sample information. E.g., a sample may by split and run across multiple sequencing lanes represented by different read groups but the same sample tag.
• Tag allows custom input of a two-letter tag as designated in the SAM format file header section. E.g., CN designates the name of the sequencing center producing the read.
  • The UCSC YC tag is supported for user-defined colored tags in RGB intensities as detailed here.
• Bisulfite mode with six options: CG, CHH, CHG, HCG, GCH, and WCG. Details are here. The rules for what constitute a mismatch to the reference genome are adjusted to account for the expected C to T (and for the reverse complement G to A) conversions. A red C or G indicates a protected site, such as by methyl modification, while a blue T or A indicates bisulfite conversion of an unprotected site.

Open anoter panel centered on the mate of the clicked alignment.

Loads coverage data for an alignment track. To generate coverage data, use igvtools. more...

Loading an alignment track from the IGV data server (File > Load from Server) automatically loads the matching coverage data.

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Clears the outlines that show paired reads.

• Control+click (Mac: Command+click) a read to outline the read and its paired mate in the same color. Colors are arbitrary but unique to each pair. A black outline indicates that the selected read has no mate.
• To clear the outline for a paired read, Control+click (Command+click) either read.
• To clear all outlines, right-click and select Clear selectionss

The selected read is used in a BLAT (BLAST-like Alignment Tool) search within the given genome as detailed on the BLAT Search page.

• Search with sequences of up to 8 kb in length.
• The default BLAT server is hosted at the UCSC Genome Browser and supports most UCSC derived genomes including human and mouse genomes. Change the default search server in Advanced Preferences.

Calculates the concensus sequence for the region in view and copies the information to the clipboard. The method for calculating the consensus is taken from Cavener, Nucleic Acids Res. 15, 1353-1361, 1987.

1. If the frequency of a single nucleotide at a specific position is greater than 50% and greater than twice the number of the second most frequent nucleotide it is assigned as the consensus nucleotide.

2. If the sum of the frequencies of two nucleotides is greater than 75% (but neither meet the criteria for a single nucleotide assignment) they are assigned as co-consensus nucleotides.

3. If no single nucleotide or pair of nucleotides meets the criteria,  assign an 'N'.

Information copied to the clipboard includes:

• Locus of the copied sequence (i.e., region currently in view)
• The consensus sequence.
• A matrix with the details of all nucleotide counts used to calculate the consensue sequence. Rows in the matrix correspond to the bases along the sequence. The values in a row show the counts for each type of nucleotide at that locus. A header row above the matrix indicates the order of the nucleotide columns (A, C, G, T, and N).