Annotation Codes

Oligos are annotated (in annotation_codes and other_annotations fields) as follows:

annotation_codes:
Code Type Definition
P Paralog Both 20b segments at the end of the oligo have >1 perfect match within the genome AND match in opposite orientation AND at <1kb apart.
W Whole Genome 20b at end of oligos exactly match whole genome more than once.
A AluI 14b internal to the ends of the amplicon sequence are perfect matches to the AluI consensus in reference file
R Other Repeat 14b internal to the ends of the amplicon sequence are perfect matches to another repeat present in the reference file
other_annotations:
Code Type Definition
W1 Whole Genome/1 20b at end of oligos match whole genome more than once, with a single base mismatch allowed
counts:
Name Definition
paralog number of paralog matches for this oligo within the genome
W0_count the sum of the number of whole genome exact matches for this oligo, for ends adjacent to RE sites (i.e. not a flap)
W1_count the sum of the number of whole genome matches (with one base mismatch) for this oligo, for ends adjacent to RE sites (i.e. not a flap)

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