Quality Control and Filtration Checks

3SeqP02

P-value from 3-seq > 0.2.

russPval005

False-discovery rate (FDR) of the parsimony improvement > 0.05. (See Supplementary Text S3 of RIPPLES for details of the null model.)

Alt

"Alternate": Other recombination trios with the same recombination node have more parsimony improvement, fewer possible breakpoint intervals, or better P-values.

cluster

All recombination informative mutations occur within a span of 20 nucleotides.

redundant

More than two of the recombination node, donor node, and acceptor node appear in that of another trios.

Informative_sites_clump

More than 5 recombination-informative mutations in a 20-nucleotide span.

Suspicious_mutation_clump

More than 6 mutations (or 3 near indels) in a 20-nucleotide span on any of the donor node, the aceptor node or the recombination node.

Too_many_mutations_near_INDELs

Too many mutations on 100-nt spans near indels or a string of Ns.