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Figure 5 shows the accuracies of MixSIH, ReFHap, FastHare, and DGS for each dataset: filtered with cluster length and heterozygous calls (filtered); further filtering with CSP (filtered+CSP).
Further filtering with unambiguous chromosome positions on the UMD3.1 assembly retained 756,243 and 42,603 effective genotypes for the BovineHD and BovineSNP50 arrays respectively.
The highest scoring result for each BLAST analysis was parsed out for further filtering, with criteria based on the method described by Seluja and co-workers [ 3]: (1) vector sequence occurs at either end of the EST, (2) the matched stretch is longer than 12 bases, and (3) shares cloning vector sequence identity of >95% for those EST pre-cleaned with Phred.
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We hereafter represent the SNP fragments filtered with cluster length and heterozygous calls as "filtered", and the SNP fragments further filtered with CSP as "filtered+CSP".
These were further filtered with various parameters to construct input files for population genetic and phylogenetic analyses (Supporting Information Table S1).
SVs inferred by no less than 3 reads were further filtered with the following conditions: (1) more than four supporting split reads or (2) no fewer than three discordant read pairs.
To improve quality, the questions were further filtered with the Stanford parser.
The intramolecular cross-links are further filtered with the following criteria using the software pLink.
The NC solution was then further filtered with a 0.25 μm syringe filter to remove excess CTAB.
The ΔNe is further filtered with different window size (WS, in seconds), as presented in panels (c)–(h).
The latter is further filtered with a 80-year running averages filter to obtain what we call the steady variation (E80).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com