Ion Torrent BAM files follow the conventions of the SAM/BAM Format Specification Working Group. SAM stands for Sequence Alignment/Map. .

The purpose of this section is to highlight specific Ion Torrent conventions and the meaning of custom tags.

Ion Torrent Conventions:

• Run ID: Every TS analysis gets a run ID, a 5-character string consisting of upper case letters and numbers, assigned. A reanalysis of a specific run will get a different run ID assigned. Example: 0JU8V.

• Read Group ID: For non-barcoded runs the read group ID is equal to the run ID. For barcoded runs it is a combination of the run ID and the barcode name, separated by a dot. Example: 0JU8V.IonXpress_001.

• Key Sequences (KS): For non-barcoded runs, the key sequence tag is the Ion Torrent library key (TCAG). For barcoded runs the KS tag entry includes the barcode sequence and the barcode adapter sequence if barcode trimming is enabled.

• SAM record (read) names: Read names are a combination of the run ID and the chip coordinates of the well that produced the read. The coordinate values are 5-digit numbers and are given in the order row and the column, separated by a colon. Example: 0JU8V:01308:00107.

• BAM header comment lines (CO): Comment lines in the BAM header are used to store base calibration information, or information about the 3' adapter sequences.