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XA
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Z
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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).
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XM
|
i
|
The target length, that is, the number of reference bases spanned by the alignment.
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XS
|
i
|
The alignment score of the next-best suboptimal mapping.
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ZA
|
i
|
The number of library insert bases, where the library insert is defined as the sequence after the 5' trimmed region (sequence in tags KS, ZK, ZT, ZE), and before the 3' trimmed region (sequence belonging to the 3' adapter, and the content of the tags SK, YK, YT, YE). Present only if a 3' adapter was found.
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ZB
|
i
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The number of overlapping adapter bases. Present only if a 3' adapter was found.)
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ZC
|
B:i
|
A vector of the following four values (present only 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.
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ZF
|
i
|
The zero-indexed flow position corresponding to the first template base after 5' trimmed region.
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ZG
|
i
|
The zero-based flow during which the first base of the adapter was incorporated. (Present only if a 3' adapter was found.)
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ZM
|
B:s
|
Normalized signals, which include phasing effects. Stored as floor(256*value).
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ZP
|
B:f
|
The estimated phase parameters for the read. The values are stored in the order CF (carry forward), IE (incomplete extension), and DR (droop).
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ZT
|
Z
|
The trimmed 5’ unique molecular tag sequence. Written only if a tag was trimmed.
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|
YT
|
Z
|
The trimmed 3’ unique molecular tag sequence. Written only if a tag was trimmed.
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|
ZE
|
Z
|
The 5’ trimmed sequence removed by the extra-trim-left command. Written only if a sequence was trimmed.
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|
YE
|
Z
|
The 3’ trimmed sequence removed by the extra-trim-right command. Written only if a sequence was trimmed.
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ZK
|
Z
|
The trimmed 3' portion of read group specific identifiers that can vary within a read group. Written only if a tag was trimmed.
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|
YK
|
Z
|
The trimmed 3' portion of read group specific identifiers that can vary within a read group. Written only if a sequence was trimmed.
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