For the de novo libraries we removed all reads showing traces of adaptor sequences, whereas for the mapping libraries we trimmed reads showing similarity to adaptor sequences and retained the read if it was longer than 30 bp.
Under the normal trimming scheme we trimmed the 5' and 3' ends of the reads with quality scores of lower than 20 (or 0.01 probability of error), then we retained the reads between a minimum length of 40 nt and a maximum of 85 nt with no further trimming (full filtered length).
Pseudo-forming – mutation results in formation of a pseudogene in one strain; coding change – mutation results in a change to the translated amino acid sequence but retains the reading frame; * fusion of two genes, retaining the reading frame.
In the case of patient #22, thirteen deleted bases were replaced by a single 'C' thereby retaining the reading frame.
However, in mono-, di- and tetranucleotide repeats, most deletions result in frame-shift mutation, which are usually deleterious; only deletions of a multiple of three units retain the reading frame.
Clone D from KYM-1 cells showed both fragment lengths corresponded with an un-edited fragment length, and this was confirmed by the sequence data, which showed a single nucleotide alteration in both alleles; this mutation disrupts the FauI site, but retains the reading frame, suggesting that EZH2 remains expressed (and likely functional) in these clones.
This filter removes those duplicate reads within a 6 × 6 window with similar sequence (allowing eight mismatches), and retains the read with the highest 'chastity'chastity
Reads from pairs with one good read and one bad read retained the good read for the largest assembly.
In the alternative transcript (referred to hereafter as PEX5 LPLvar), splicing was from within the PEX5 intron 1 2 into LPL exon 4. The transcript retained the LPL reading frame, and therefore, could also encode a full-length chimeric protein.
The sequences in the GSS collection from which the consensus was built represented unedited submissions, and excluding single base indels that might have been the result of unedited miscalls, most of the indels in the ORF retained the correct reading frame.
