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G12 which interacts with the cleavage site, is mutated in only one sequence.
To facilitate data processing, we established a cutoff for GO terms that were present in only one sequence within the DAG generated (data not shown).
It is worthwhile noticing that 12 out of the 44 types appear in only one sequence, which account for 10% of the binding sites.
Tyr9 is substituted in only one sequence (by Phe), and Pro5 is replaced by Tyr or Phe in two sequences from Mycobacterium species.
With few exceptions, singletons, i.e. variant nucleotides found in only one sequence, were ignored.
Extreme 5' and 3' sequence ends, which were often of uneven length and poorly aligned, were excluded, as were indels present in only one sequence.
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In general, the artifacts do not confound data interpretation, as they are typically minor and apparent in only one sequencing direction.
The first filter – the "reliability filter" – removes any signature that is observed in only one sequencing run across all libraries, with the aim of eliminating signatures that result from technical problems specific to a single sequencing run.
The signature sets were filtered to remove any signatures that were 1) not reliable: observed in only one sequencing run, and 2) not significant: never observed at or above 4 tpm in either library.
The signature sets were filtered to remove any signatures that were not 1) reliable, i.e., observed in only one sequencing run, and 2) not significant, i.e., never observed at or above 3 transcripts per million (TPM) in either library.
a MPSS signatures within exons, within 500 bp of an annotated gene, in an intron, and overlapping an exon-intron splice boundary were quantified and "insignificant" signatures in only one sequencing library and those signatures corresponding to multiple regions of the genome were removed to demarcate gene expression.
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