XA

Z

The algorithm that produced this mapping and from what stage. The format is the algorithm name and the zero-based stage (separated by a dash).

XM

i

Target Length, i.e., number of reference bases spanned by the alignment.

XS

i

The alignment score of next-best sub-optimal mapping.

ZA

i

Number of library insert bases, where the library insert is defined as the sequence after the key and barcode adapter, and before the 3' adapter. (Only present if a 3' adapter was found.)

ZB

i

Number of overlapping adapter bases. (Only present if a 3' adapter was found.)

ZC

B:i

A vector of the following four values (only present if a 3' adapter was found):

Field 1: The zero-based flow during which the first base of the adapter was incorporated (same as ZG)

Field 2: The zero-based flow corresponding to the last insert base

Field 3: Length of the last insert homopolymer

Field 4: Zero-based index of adapter type found.

ZF

i

The zero-indexed flow position corresponding to the first template base after 5' trimmed region.

ZG

i

The zero-based flow during which the first base of the adapter was incorporated. (Only present if a 3' adapter was found.)

ZM

B:s

Normalized signals, which include phasing effects. Stored as floor(256*value)

ZP

B:f

Estimated phase parameters for the read. The values are stored in the order: CF (carry forward), IE (incomplete extension), and DR (droop).

ZT

Z

The trimmed 5’ unique molecular tag sequence. Only written if a tag was trimmed.

YT

Z

The trimmed 3’ unique molecular tag sequence. Only written if a tag was trimmed.

ZE

Z

The 5’ trimmed sequence removed by the extra-trim-left command. Only written if a sequence was trimmed.

YE

Z

The 3’ trimmed sequence removed by the extra-trim-right command. Only written if a sequence was trimmed.