Only non-synonymous mutations were kept for further downstream analyses.
The positions of the cysteine mutations were kept as consistent as possible among the three proteins (Table 3 and Figure 2) to facilitate comparisons.
These mutations were kept out by the application of chosen variability and/or disease score thresholds but were retained by the other filtering steps.
Fish harboring frame-shift mutations were kept and used to raise F2 mutant lines, i.e. the ascl1b ulg-M2C and nkx6.1 ulg-M5 lines carrying, respectively, 11 and seven nucleotide deletions.
During each iteration of the LOO-unseen, a single mutation was kept for testing and the rest of the mutations in the query position were used for training.
In each iteration of both procedures, one query mutation was kept as a test and the rest of the mutations were used for training.
Therefore, as a single gene usually has multiple TFBS, and more types of mutations occur on TFBS than on genes, TFBS mutation rates are kept somewhat lower than gene mutation rates.
Virgin female flies, with the transgene or mutation of interest, are kept at 10° for 7 d.
To obtain rare and deleterious variants, variants with a minor allele frequency greater than 0.01% in either 1000 Genomes and the Exome Sequencing Project data are removed and only nonsynonymous mutations, frameshifts, and stop-gain/losses are kept.
