After the Q-score is determined, results are recorded in the base call files.
Sequencing Output Files
File Type File Description, Location, and Name
Base call files Each tile analyzed is included in a base call file, aggregated in 1 file for each lane, for each cycle. The
aggregated file contains the base call and encoded quality score for every cluster for that lane.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
[Cycle].bcl.bgzf, where [Cycle] represents the cycle number in 4 digits. Base call files are compressed
using block gzip compression.
Base call index file For each lane, a binary index file lists the original tile information in a pair of values for each tile, which
are tile number and number of clusters for the tile.
Base call index files are created the first time a base call file is created for that lane.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
s_[Lane].bci
Cluster location files For each tile, the XY coordinates for every cluster are aggregated into 1 cluster location file for each
lane. Cluster location files are the result of template generation.
Data\Intensities\L00[X]—Files are stored in 1 folder for each lane.
s_[lane].locs
Filter files The filter file specifies whether a cluster passed filters. Filter information is aggregated into 1 filter file
for each lane and read.
Filter files are generated at cycle 26 using 25 cycles of data.
Data\Intensities\BaseCalls\L00[X]—Files are stored in 1 folder for each lane.
s_[lane].filter
InterOp files Binary reporting files used for Sequencing Analysis Viewer (SAV). InterOp files are updated throughout
the run.
InterOp folder
RTA configuration file Created at the beginning of the run, the RTA configuration file lists settings for the run.
[Root folder], RTAConfiguration.xml
Run information file Lists the run name, number of cycles in each read, whether the read is an indexed read, and the
number of swaths and tiles on the flow cell. The run info file is created at the beginning of the run.
[Root folder], RunInfo.xml
Thumbnail files A thumbnail image for each color channel (red and green) for tiles 1, 6, and 12 from all cameras, top
and bottom surfaces, at every cycle during imaging.
Thumbnail_Images\L00[X]\C[X.1]—Files are stored in 1 folder for each lane and 1 subfolder for each
cycle.
s_[lane]_[tile]_[channel].jpg—In the file name, the tile is represented with a 5-digit number that
indicates surface, swath, camera, and tile. For more information, see
Tile Numbering
on page 44 and
Thumbnail Image Naming
on page 45.
Flow Cell Tiles
Tiles are small imaging areas on the flow cell defined as the field of view by the camera. The total number of
tiles depends on the number of lanes, swaths, and surfaces that are imaged on the flow cell, and how the
cameras work together to collect the images.
u High-output flow cells have a total of 864 tiles.
u Mid-output flow cells have a total of 288 tiles.
Document # 15046563 v04
For Research Use Only. Not for use in diagnostic procedures.
42
NextSeq 500 System Guide
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