Well-Level Signal Data Files (.wells)

2. Data Files and Formats : 2.3 Standard File Formats : 2.3.4 Well-Level Signal Data Files (.wells)

2.3.4

Well-Level Signal Data Files (.wells)

The wells data file is a legacy binary file containing counts values for the light collected on the nucleotide and PPi images, at each “active” well location. The file consists of a header and a body, where the header contains the following fields:

unsigned int numWells;

unsigned short numFlows;

char flowOrder[numFlows];

…where numWells is the number of wells (or reads) in the file, numFlows is the number of flows in the sequencing Run script, and flowOrder are characters indicating the reagent for each flow: ‘A’, ‘C’, ‘G’ and ‘T’ specify each nucleotide flow, and ‘P’ signifies a PPi flow.

The body of the wells data file contains numWells records of the following fields:

unsigned int rank;

unsigned short x;

unsigned short y;

float flowValues[numFlows];

…where rank is the general ranking of the well (by signal intensity); x and y are the coordinates of the well center pixel; and flowValues are the signal values for all the flows in this well.

All the multi-byte values in the header and body are written using little endian byte ordering (consistent with the Linux operating system). As these are binary-format files, an example cannot be provided in this text-based document.